Ule CLIP Supporting Online Material Science2003

Supporting Online Material:Materials and MethodsFigures S1,S2Tables S1, S2.

Materials and Methods

CLIP Method. See http://www.rockefeller.edu/labheads/darnellb/newrsrch.htm

Computer analysis of Nova CLIP tags. 3400 control tags were randomly

generated by a computer program from a 200,000 nucleotides long sequence consisting

of 66% intronic, 14% exonic and 20% 3’UTR sequences (corresponding to the ratio in

Nova CLIP tags) from random genes on mouse chromosome 1, such that they

corresponded in their size to Nova CLIP tags (with the average size of 71 nucleotides).

Another program was made to count the number of particular polynucleotide (up to 20

nucleotides in a row) in each tag, and calculate the frequency of tags carrying a certain

number of that polynucleotide (for example, YCAY, where Y represents either U or C).

Additional program was made to calculate the average frequencies of nucleotides at three

positions flanking a particular dinucleotide (CA in our case) in all tags.

Nova-2 protein purification. 6xHis-Nova-2-T7 protein was expressed in E. coli

and purified with successive Chelating Sepharose fast flow column (Amersham 17-0575-

01) and T7-tag antibody agarose (Novagen, 69026).

Transcription of Oligonucleotide Templates. The PCR products for each of the

four tested CLIP tags and genomic controls were annealed to the oligonucleotide 5'-

AGTAATACGACTCACTATAG-3' for transcription with T7 polymerase (Promega),

and RNA synthesis carried out by using α-32P-UTP in standard transcription buffer

(Promega). Transcripts were size-purified by using 20% denaturing PAGE.

Measurement of RNA-Protein Binding. Binding dissociation constants were

measured by a nitrocellulose filter binding assay (1). 50-µl reactions containing 50-100

fmol of RNA internally labeled with 32P and concentrations of Nova-2 in 3-fold dilutions

typically ranging from 0.2 nM to 493 nM were mixed in 1 xBB (50mM TrisOAc pH 7.7,

200mM KOAc, 1mM MgOAc, 1mM DTT, 0.2 mg/ml heparin) and were incubated at

1

10 min for 25°C, followed by filtering and washing. Dissociation constants were

determined graphically by plotting the fraction of bound RNA versus the log of the

protein concentration (2).

RT-PCR analysis was performed as described (3). PCR of mouse JNK2 was

performed at Tm=60°C and 26 cycles, with primers F, 5’-

TGATGACTCCCTATGTGGTAACTCG and R, 5’-

TCTCTGGCTTGACTTGTTTTTATTTTG, and PCR products were digested with Rsa1;

we also tried digesting products with Alu1, which resulted in same quantitative difference

between isoforms (data not shown). PCR of mouse neogenin was performed at

Tm=61°C and 23 cycles, with primers F, 5’- ACACTGGCTGGAAGGAGGGG and R,

5’- TGGGCTGTGGGAAGACTCTGG, and of mouse gephyrin at Tm=61°C and 23

cycles, with primers F, 5’- TGTGGAATAAGGGGGAAAACTCTG and R, 5’-

TCGTGGGAGCACCTGAACAC. Clontech first strand cDNAs were used for analysis

of splicing in mouse tissues.

Immunoblot analysis. The following antibodies were used: gephyrin

(Transduction laboratories), rabbit Nova antiserum (4), Hsp90 (Transduction

laboratories), rabbit brPTB antiserum (5).

References:

1. J. Carey, V. Cameron, P. L. de Haseth, O. C. Uhlenbeck, Biochem 22, 2601(1983).

2. D. Irvine, C. Tuerk, L. Gold, J Mol Biol 222, 739 (1991).3. K. B. Jensen et al., Neuron 25, 359 (2000).4. R. J. Buckanovich, R. B. Darnell, Mol Cell Biol 17, 3194 (1997).5. A. D. Polydorides, H. J. Okano, Y. Y. Yang, G. Stefani, R. B. Darnell, Proc Natl

Acad Sci U S A 97, 6350 (2000).

2

Figure legends

Figure S1 Distribution of tags relative to number of YCAY tetramers they contain.

Figure S2 RT-PCR analysis of gephyrin exon 9 splicing in indicated mouse tissues.

Table S1 Annotated list of 340 Nova CLIP tags. CLIP data available athttp://www.rockefeller.edu/labheads/darnellb/newrsrch.htm

Table S2 A list of Nova CLIP tags belonging to transcripts coding for proteins with arole in inhibitory control.

Distribution of tags relative to YCAY content

0

10

20

30

40

0 1 2 3 4 5 6 7 8 9 10 12 14 16 18 20# YCAY tetramers per tag

% o

f to

tal t

ags control tags

Nova CLIP tags

Hu CLIP tags

Figure S1

test

is

kidn

ey

skin

liver

lung

sple

en

brai

n

hear

tNon-N

N

Figure S2

Other R

NA

targetsFunctional N

ova-binding site (defined by mutagenesis)

PositionC

hange inN

ova 1 KO

spinal cord

Reference

Function

GA

BA

A γ2C

UC

AU

UU

UC

AG

AU

UC

AU

CA

UC

UC

AIntron 9

decrease inexon 9inclusion

MC

B23:4687-4700

Inhibitory receptor

GlyR

α2

UC

UC

AU

CA

UC

AU

UU

UC

AU

UU

Intron 2decrease inexon 3ainclusion

Neuron 25:

359-71Inhibitory receptor

Table S2: A

list of Nova targets w

ith a role in inhibitory controlC

LIP

RN

AT

argetC

LIP

tagC

LIP

tagposition

Change in

N2 K

Ocortex

Reference

Function

GA

BA

(B)

2 receptor

AC

UG

UC

CC

UC

CC

CA

UC

UA

CU

CA

CU

GU

CU

UC

CC

CA

UC

UA

CU

CA

CU

GU

CC

UC

CC

CA

UC

UA

CU

CA

CU

GU

CC

UC

UC

AU

CU

AC

UC

AC

UG

UC

CU

CC

CA

UC

UA

CU

CA

CU

GU

CC

CU

CC

CC

AU

CU

AC

UC

AC

UG

UC

CC

UC

CC

CA

UC

UA

CU

CA

CU

GU

CC

UC

CC

AU

CU

AC

UC

AC

UG

UC

CU

CC

CC

AU

CU

Intron 7Intron 7

noneS

cience283;74-7

Stim

ulation of GIR

Kchannnels.

GIR

K2

channel

GC

AA

GA

CA

UG

GC

UG

CC

AU

CA

CA

UC

CC

UC

AC

CA

CU

GU

CA

UG

AU

AA

UC

AU

CC

AU

UC

UU

AU

CC

CU

GC

UU

GG

AC

AC

CA

AG

UG

UC

UG

CA

UU

UG

GU

GG

CU

GA

UU

AC

GG

GA

UG

GA

UC

CC

UG

GG

UG

UG

GU

UG

UC

UC

UG

CA

UG

GU

CC

AU

CC

UU

AU

CA

GU

U

Intron 2Intron 2

noneN

euron19:687-95

Generation of slow

inhibitorypostsynapticpotential.

Gephyrin

CC

AG

UU

CA

AC

CA

CA

GG

UC

CC

CA

GC

UU

CC

AU

CC

AU

UG

GU

UG

GG

UG

CU

AG

UA

UC

UG

CA

UC

UG

AC

UC

UU

UC

AG

CU

CC

AA

CC

AC

AA

AU

GC

CA

GC

AC

CU

CU

UA

AU

AA

CA

AU

CA

GC

AU

GA

CC

UC

UG

CC

UA

AG

UC

UU

GG

CU

UC

UU

CC

UC

AG

AA

Intron 7Intron 15

60X increase

in exon 9inclusion

Nat R

evN

eurosci4:251-65

Scaffold of inhibitory

synapse.

MA

P1b

AA

GU

GG

CA

GA

UU

CA

CG

UC

CC

AG

GG

UU

CA

GA

GG

UG

GC

AA

AC

UU

CU

CA

GU

GG

CA

GC

UG

UG

CU

CG

GU

CA

UG

CA

GA

UU

UC

GA

GU

UA

CU

GC

AA

AA

UU

GC

CU

AC

CC

CC

GU

UC

AU

CU

CU

GC

UG

AA

CA

UU

CG

GUA

CA

UA

GU

CA

GG

GG

AG

GG

CC

CC

UG

UC

AA

CG

UG

CC

CA

CA

AG

GU

UC

CU

UU

AU

CC

UU

UG

UC

AU

UA

CG

UC

AU

UG

UC

CA

AG

GU

GA

CA

GG

AG

GA

AC

UC

AG

UC

GU

UA

AA

AU

GA

CG

AG

CC

UU

AU

UU

UC

AU

GA

Intron 23’ U

TR

3’ UT

R

noneJ N

eurosci20:8643-50

Modulation of

GA

BA

(C) receptor

current

KC

NQ

3C

CU

GA

CG

GA

UC

CU

GU

GA

CG

CC

CA

CA

GU

AU

CC

CU

GU

AG

CA

GA

CU

GG

CA

UG

GC

CU

UG

CC

UG

UG

AG

AU

UU

UA

UU

CC

UC

UC

UC

CC

AG

UC

CA

CC

CU

CC

AA

CU

GU

UC

CA

CA

UC

CC

AU

AC

CU

CC

UC

CC

UA

CG

CC

AU

GU

UU

UC

AU

GA

GG

AU

GU

CC

UU

CC

CC

UC

CA

CC

CA

CU

CC

AC

Intron 13’ U

TR

noneA

m J M

edG

enet;106:146-59.

Inhibition ofrepetitive actionpotentials bym

ediating M-current.

Nicotinic

AC

hR β

2

GG

UG

GG

AA

AG

UA

CC

UC

AU

GU

UC

AC

CA

UG

GU

GC

UA

GU

CA

CC

UU

CU

CC

AU

CG

UC

AC

UA

GC

GU

GU

GA

CA

CC

AU

CA

AC

CU

CA

UC

AU

CC

CC

UG

CG

UA

CU

CA

UC

AC

CU

CG

CU

GG

CC

AU

CC

UG

GU

CU

UC

UA

CC

UG

CC

Exon 5

Exon 5

noneN

euron31:131-41; JN

europhys87:3117-25

Activation of

GA

BA

ergicinterneurons, part ofA

crb2/Acra4 receptor

Nicotinic

AC

hR α

4

UC

AA

UG

UA

CA

CC

AC

CG

CU

CA

CC

AC

GC

AC

AC

AC

AC

CA

UG

CC

CG

CC

UG

GG

UG

CG

CA

GA

GU

CU

UC

CU

GG

AC

AU

UG

UG

CC

CC

GU

CE

xon 5none

ibidP

art of Acrb2/A

cra4receptor

Jnk2G

UG

UU

CU

UC

CA

UU

UU

CC

AC

AU

UC

UU

CA

CG

CU

AA

CA

UG

CG

UC

UU

CA

UG

CU

Intron 66X

increasein exon 6a vs6b inclusion

EM

BO

J20:5114-28.

Regulates G

AB

Aaction in C

. elegans

Table S1: Annotated list of 340 Nova CLIP tags

CLIP tag sequence gene name location in genome location in transcript detailed location

ACCCAACTGCTTAGCAGTGTGGAGCAGACTGGAGGAATCACTTTTCTTGCTTGCATCACATGCTGCCCCCTGT

BAI 3 chr1:25714835-25714907

intron 11 (200 kb) 90 kb 5' to exon 12

TCACGCTTCCTCTGAAAACACATTGCACCCTCCACCCGCCACCCCTTCACCCTCCACCCGCC

Rab23 chr1:34189409-34189470

intron 2 200 b 5' to exon 3

TGAATTCCAGGACACCTGAGGACATAAAGGAGATTTTAAGAAAACAACCATCATCATTATCTTGTCGTCATCATCATCTGCATCTGC

clone C40 unknown mRNA chr1:40049118-40049204

intron 3 400 b 5' of exon 4 (part of B1_MM, Alu, SINE repeat element)

CACTCCAGCCATCACTGCCTGTGCTTGCTGCAGATGTTCCTGCTACCTGCTTTGCTGAGTCTGTA

cytochrome P450 monooxygenase

chr1:60972292-60972358

intron 4 (9kb) 1.5 kb '3 to exon 4

TCACACAGTCCCCAAGCAGGTCCAGCGTGGCATCACCCCGACGACCAGCAACGTCTCATCTTCTGGAAGCA

microtubule-associated protein 2 (MAP2)

chr1:67069834-67069905

3' UTR

TCGAACTCAGAAATCCACCTGCCTCTGCCTCCCAAGTTCTGGGATTAAAGGCATGCAGCCCCATTACCA

ribulose-5-phosphate-epimerase

chr1:67340700-67340768

intron 2 (8kb) 3 kb 3' to alternative exon 2

TTCAGCTTGCAGCTGTCATCTCTCTGCTGTTCCCAGCTGTC BARD1 (BRCA1 associated RING domain)

chr1:71775451-71775491

intron 1 (13 kb) ~ 2 kb from exon 1

TGTTATTAGTTTCCATCCATTCATCCATCAATCCATTCATCCATTTACCTATGCATTACCTAACCACCCTTCTCCATCCCTCC

KIAA1486, similar to Myosin heavy chain Myr 8b

chr1:81995681-81995763

intron 3 (104 kb) 37 kb 3' of exon 2 (both exon 2 and 3 are alternatively spliced?)

ATGCCTCGGCACTCCCTCTACATCATCATCGGAGCCCTCTGCGTCGCCTTCATCCTCATGCTCATCATCCTGAT

transmembrane protein Bet chr1:85272953-85273026

exon 12 240 b 5' to stop codon (in exon 13)

GTGTTTGATCATGTCTTCCACTGCTCCCTGCCCCCAGCTCCTCCCAGAGCCTCCCACTTGGCTTCCAGCCC

GAP2 chr1:132126421-132126491

intron 17 (3 kb) 500 b 5' to exon 18

AATTCATTCATTCATTCACTCTCTCTGTGTGTCTCTCCCTGTCTCTCTGTCTCTGTCTCTCAGGA

no gene predicted chr1:133829086-133829149

repeat element included

GGAGGCGTGCGAAGGTAGGCTCAGAAATGGCCCTACCTCACCTTCACCTCTCACTCTGCTTCATGCTT

KIAA0969 brain protein chr1:134134914-134134955

intron 10 (2 kb) 1.5 kb 3' to alternative exon 10 (5' part of sequence bacterial)

CCTCATCCTGCCTCCCTGCATCCCAGCTCCTGTGGCCTCATCCTGCATCCCAGCTCCTGTGGCCTCATC

no gene chr1:136304233-136304301

duplicated sequence

GAGGGCCCACCCCATTCCCATTCTACATCTACCAACTTCATGGCAAATCATTACAATAGTCTCTGCATTTCCAGT

N2,N2-dimethylguanosine tRNA methyltransferase-like

chr1:152370289-152370356


TCAGTTCATCCCTATCCATCACCCTGGAGCCTTCCCTCCTCTTCC

KIAA0250 gene product ~chr1:153780180 exon 10

GCCAGTGGCTGAGGACATGACAGTCCACTTCACCTCCACACTTATGGCTCTGATCCGGACAGCTCTGGAC

voltage-dependent alpha-1 E calcium channel

chr1:155359770-155359839 intron 20/exon 21 junction alternative exons 20, 19

AGCTGTGCGGCTTACATGGCAGACGCTCCAACGTGTATTCAGATGCTCTGGCTGCATCCCTTCCCA

FLJ31744 chr1:156228475-156228540

(3' UTR)

ACAGGGCGACGTTCCAGGCCAAGTGATGTGATTGTGAAGACCCCATGTCCTGTGGTGGATGA

astrotactin chr1:159800711-159800772

exon 18

GCTTCCCTAGCGCAGGCAGGAACTGATGACAGGCCATGGAGGAGTGCTGTCTATCTCCACCCTGCCTCCCCTCA

HSPC163 brain protein chr1:182547933-182547985

intron 3 (6 kb) 3 kb 3' to alternative exon 4 (misalignment)

ACACTTCTCCCAGTGGTCACTCTGGCTTTGATCACACCTCATTGGGTGGCTCCTTAGCAGTGTTGGACA

no gene prediction chr1:196518134-196518202

ATCTTCATGCCCGTTAGTCATCGTTTGCCTAGCATGTCCCTGTGGCGTCTCAAAAACAGTTTCATCGTCCCGTC

apoptosis-related RNA binding protein (Napor-1)

chr2:6553077-6553150

3' UTR

GAGATCCTTAGGACCTCTCGAGGTCTTCACCAAGCCCTGCATCTCCCATCCCATCTATCTTCTCCATCC


GCACCTCCTTCCTCTTCATCACATCTCACTTCACCTCTGGAGATGGGAAGGTAGCAGAGCGGCTACTGG

inositol polyphosphate 5-phosphatase

chr2:26685978-26686275

exon 5/6 junction

CAACTGCAGCCCTCGGCTCCTTCCTTCCCACCTCCGACACATCTCCTCTCTTCTCGCATCCCTCCTCAG


3' UTR

CAGCAATGGAGGAGTGTTCCTCTTTCTTCACATCCTCACCAGCATCTGCTGTCACCTGAGTTTTTGATC

hippocampal EST chr2:39551345-39551413

intron

TACTACTCATCTTGCAGATGTCTACCCATCTGTCCCTCCTCACCTGCTTCCG

voltage dependent Ca++ channel beta 4

chr2:53125936-53126038


ATCTTTGCCTCCTCACTCATCAAAACTCATCTGTAGCATGGCTTTCATCCATAGATTCTCAGGGGAATCACTTAACATCCATAGTCTCA

erg3 (the ether-a-go-go-related K+ channel)

chr2:63842508-63842596


CGTTCTCTTGCTCATCTCCGAGTTCTGCCTTGCCCCTCTCAGATG

G protein-coupled receptor msr/APJ

chr2:86042431-86042475


CTGCAGAGCTCACTGCATTCACCCCTCCTCATCCTTTGCTTCCTTCCCCTTGCCTAGTCAGTAG

apoptosis inhibitory protein 5 = FGF-2- Interacting factor

chr2:95399493-95399556

3' UTR 1.9 kb 3' to stop codon

ACCACACCTGTCTCCTCCTTCACATCAGGTTCCATGTTGGGCCGAACAGACACCGCCCTCACCAACACGTACAGTGC

Pax6 paired-less isoform mRNA

chr2:106611345-106611537

exon 9-10 junction covering alternative part of exon 9, 10

CCATCCCCCCATACCATCTCTGAATCTCCTTCCCCTCCTCATCTCAG

TALE homeobox protein Meis2b

chr2:116796803-116796850

intron 10 200 bp upstream from alternatively spliced exon 11

CCATCTCACCCCTGCCTTCTCCTCCATCCCATCCCTGCCTTCCCCTCTAT

similar to erythrocyte protein band 4.1-like 4

chr2:122564425-122564474

intron 6 2 kb 3' to exon 6 (part of (GGATG)n repeat element)

CATCCATCTTGACTCATTGCTGTCACTGCAGAAGGACTAAGTAGCAAAACACTGCTCCAAGGTCTTTGGC

similar to TULIP-1 chr2:147362783-147362852 intron 19 (5 kb) 1 kb 5' to exon 20

AAACAACATGTCCCCTGCAACATAATCCATGTTCTTCCTGTCATTCCACCATCCCTGACCCCACCCCCTCCAC

similar to TULIP-1 chr2:147387288-147387363

intron 11 (8kb) 1.5 kb 3' to exon 11

TTTCACTCCACCTGCTATCTTGACTTGACTC no gene prediction chr2:150411042-150411072

ACTTCTGGGGTCTCATGATTTCCCCATCTAAGACCTTAGTCCACCTGAACCAGCGTTTCTGTCTGTGTCCAAATGTCCATCTGTTTGTCTTTTCTTCATTTC

similar to Xenopus laevis putative Zic3

chr2:156738596-156738692

intron 4 2.3 kb 3' of alternatively spliced exon 4

AGCTGAAATGTGCAGGCTTGTTGTGGCAAGTGGGCTTACCCACTGAGCCATCTCATCTACCACTTGGTGTC

transcription factor TZP chr2:157077852-157077922


GGCTTGCTCTCAATGTCTCTCCCTTTCTGAGTGAAAGTATCCCACGGCAGTCCCATCTCACTTCCTGTCCTGCTAAGGC

neuronal protein 4.1 chr2:157392230-157392308

3' UTR


CAGAGCCACCTGGAGGATGACCAGCCAGGATTGTTCAGGGCTTCATTGTCTTGGTCACATTGCTTCATTGTCT

hypothetical protein XP_149237

chr2:159256103-159256173

exon 1

ACCTCACGTGGTCAGCCATGACCAATGAACCTGAGCGGTCCTGCAATCCCTCCCTTATGAGCATCATC

membrane protein TMS-1 chr2:164560001-164561142

exon 7/exon8 junction

TCCGTCCATCCATCCGTCCATCCTTCTATCCATTCATCTATCCATCCCATGACCAGGATGAAGGTGCGGTA


intron 1 (60 kb) 12kb 5' to exon 2 (3' 18 bases of the original sequence are bacterial)

GATGTCTACTTCATTGCCACCCTGTCATTCCTCTGGAAGGTGTCCGTCATCACCTTGGTCA

putative E1-E2 ATPase (class II, type 9A)

chr2:169635729-169635789

3' UTR

TCAATGTACACCACCGCTCACCACGCACACACACCATGCCCGCCTGGGTGCGCAGAGTCTTCCTGGACATTGTGCCCCGTC

nicotinic acetlycholine receptor alpha 4 subunit (Acra4)

chr2:179360962-179361042

exon 5

TTCATTCATTCATTCATTCATTCGTTCATTTATGGTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTACACCAGGCTGGCCTCGAACTCAGAA

Nuclear receptor co-repressor/HDAC3 complex subunit TBLR1

chr3:21915734-21915849

intron 1 (30 kb) 10kb 5' from exon 1 (part of B1_MM, Alu, SINE repeat element)

AAATTATTCATCGCCATCCACCATCCACCACTCCCTCCTGCTCCACATGCTCCATTTCC

Traf2 and NCK interacting kinase (TNIK)

~chr3 28344045 intron 2 (18 kb) 6 kb from nearest exon

CTCATTACTGTGCTGTTCTGGTGAGCAGAGTCCTGGCATTATGTAGCCAGCGCCTTTCTT no mRNA

chr3:29401302-29401361

AGTCTCACCCCAGGCTGTTAGTATTCCATCAGTCTGTCCTAAGGGAGTATGTCTCATGTGCTCCTGACCCATCCCATCTACATCC

SPAF homologue chr3:37444852-37444931

intron 15 (50 kb) 20 kb 5' to exon 17 alternatively spliced exon 16

ACCCCCTCTTCAGCCTCATGTCTGACCTCCTCACCCGCCCACCATTGTTC

similar to embryonic blastocoelar extracellular matrix protein precursor

chr3:54038643-54038692

intron (11 kb) 2 kb 5' to exon

AGCTCTTTGAGCATCTACATCATCTTAGTATTTCCTCCAGAGAGGAAGTCTGGTCATGTTCCCCTTAGGTC

Trp4 Ca++ channel chr3:54761947-54762017

intron 6 1.2 kb 5' of exon 7 (exon 8 alternatively spliced)

CTGGCTTTTCCTCTGCTCCACCCACTTTCACCACTGGGCTGTTAGTCCTTCTCTTCTCAGCCTCCAGCGTTTGTACATTA

Spartin/SPG20 chr3:55593856-55593935

intron 4 800 b 3' to alternative exon 4

CATTTCAAATGTTTTCCCCCTTCTAGGCTTCCCCTCTGCAAACCCCTTAAGCCATCCTCTCCCCCCTGCTTCTATG

ring finger protein 13 chr3:58301266-58301341

intron 2 500 bp before alternatively spliced exon 3

ATGTTTTAGTTTTCACAATTACTTTCGCCATCATTTGCTTTTTACTGACAAAATGTCTGTCCATCCTTCTCATTGTCTCCCCCATCCTCAGTT

ring finger protein 13 (Rnf13) chr3:58363159-58363251

intron 8 2 kb 5' to exon 9

ATATAGAACTGTCTTCCAAGTGTGTTGAGTGTCAGGAACAACTACAGTATTGAGATCTGTAAAGAGAGAGGACTTTTTTTCAACC

guanosine 5'-monophosphate synthetase

chr3:64548922-64549049

intron 2 200 b 5' of exon 3

AGCACCAGGGAGCAAATGCCAGCTGATTGTTGTTCCTGCCCAGCTTGCTGGCTAGCTTTGATACATTCCTCA

BB642374 brain EST chr3:73684385-73684456


AGCACCAGGGAGCAAATGCCAGCTGATTGTTGTTCCTGCCCAGCTTGCTGGCTAGCTT

BB642374 brain EST chr3:73684385-73684442


ACCTCATCCCTGGCAGCCCCTTGCCTCACGTGGGTGCTGCTCTCACAGTCACTACCCACCCCCACATCAGCA

myocyte-specific enhancer-binding factor 2 (Mef2d)

chr3:88955291-88955355

exon 11

GGTGGGAAAGTACCTCATGTTCACCATGGTGCTAGTCACCTTCTCCATCGTCACTAGCGTGTG

nicotinic acetylcholine receptor beta 2 subunit (Acrb2)

chr3:90601032-90601094

exon 5

ACACCATCAACCTCATCATCCCCTGCGTACTCATCACCTCGCTGGCCATCCTGGTCTTCTACCTGCC

neuronal nicotinic acetylcholine receptor beta 2

chr3:90601206-90601272

exon 5

CTCTGTGTAGTTGTCAGGGTTCCACCTTTGCTGTCATCTCCTGGTAACGCCTCAGGTGGACCAGGGAGCAAACCTGACTCCTGATCAGCCTCTGAAGCCTACTTGGTTGCCATCTTCCGAG

no good gene prediction chr3:91344105-91344226

CCCTACCCCAGGGACCATGGTTCCTAGGATCTCACTGCCTCCCTCTCTGGCCTTCCTGTCCCCTCCC

TRH3 chr3:95610938-95611004

3' UTR

AAACCCTTCTGCCAGGTGACCACACGCAGCTTCCCTGCCCGCTCCTTCATCACCTTCCG

Flamingo 1 chr3:108897325-108897383

exon 3

AAAGTGCTTCATTTCTCCTGCCCACCCTTGCAGGTAGGGCCAGTCACTCTTCCATTGCTTCTTTGCTGT

Flamingo 1 chr3:108884460-108884528

3' UTR

GCCATCATCACCATCATCGCCATCATCACCATCATCACCATCGTCATCGCAATCTT

Cdc14 phosphatase chr3:116728088-116728142


AGTGTGAACTCTGAAATGTTCTCAGCATCCTCGTCCTCCCTGGGCCCAGAGAGTCTCATTCTCCATAGGT

AK056665 (brain protein) chr3:117673991-117674060

intron 3 (4 kb) 1.5 kb 3' to exon 3

CCATAAATTCATCCTTTGCTTCTTTCCTCAGGCTATCTTAGTAGAAATGGCATAATTGTCTTATCTACTTTGACTTATTTTTCCATTCTGA

brain polypyrimidine-tract binding protein

chr3:120099830-120099920

intron 6 2 kb 3' of exon 6 (exon 9 is spliced out in non-neuronal tissues, which produces a dominant-negative product)

CCCTGAAGAGCCATCCCACTGCCTGGCCGCCTACCTGCTGACACCACCCAGCATGGCTTGTGAACGTCACGTCAGTTCACTGCCGCA

tetraspanin Tspan-5 chr3:139299425-139299511

intron 1 (126 kb) 55 kb 3' from exon 1 (or 20 kb 3', or 12 kb 5') : alternative promoters!

ACTCCATCATCTCCTCAAAAGCTAGACCAGCCCACTGCATCCGCATTGGCTCCATTCCGTCATTGCC (Similar to) RAP1

chr3:139518271-139518337 intron 4 (30 kb)

300 b 3' to exon 4 (alternative exon 5)

AGAAGTGCAGCTTGGTCTTCATGTGGGTCTCCCAACAATTGGAGCAGGGGCTATCCCTGACTCTGTTGCCTGCCTGTGGATCCTGTTCTCCTCACTGGGCT

dimethylarginine dimethylaminohydrolase 2

chr3:146370425-146370525


CATGGAATCCTCTGCCATCAGGTTCCCATCATCATTGCTTGGG


AACACTCTGCAGGGCTGCTTGGTCTGCTGGTATCTTTTCAGTTACCACTCATGTCTCACCCCATTGTTCACATC

aspartyl beta-hydroxylase (Asph)/junctate 2/3

chr4:9086578-9086651

intron 4 15 b 3' to exon 4 (alternative exons 4a, 5)

CCGCAGGGAAGTGACTTTCACAGCTTCCGGCCTGCCTGTCCGTCTGTGTCTGTCTGTCCATTCAGTGG

polyadenylate binding protein chr4:11597662-11597729

exon 1 (5' UTR?) same as 316, 420

CCCACACCACCCCTCCACTGCTACATATTTCTAATCATTCTCTTAGCCCTCTACTTCTCTCTTGTCTCANCCCATACCTGACCC

matrix metalloproteinase 16 chr4:17623741-17623824

intron 5 2 kb 5' of exon 6

CCCGACCCCCACCCCCTTGCCTTATTCCTTCAGCGAGTG Bach2 chr4:31931113-31931151

intron 2 (50 kb) 20 kb 3' to alternative exon 2

TCAGCAGGGAAACTGGTTATCCACACAGTTCTTCACCCTCATCCTCACGTCTGTCAGCCATTCACCCGCA

AB056417 brain protein chr4:41306575-41306644


ACTGTCCCTCCCCATCTACTCACTGTCTTCCCCATCTACTCACTGTCCTCCCCATCTACTCACTGTCCTCTCATCTACTCACTGTCCTCCCATCT

GABA-B receptor 2 chr4:45617532-45617646

intron 7 (38 kb) 19 kb 3' of exon 7 (homologous exon 7 in GABAB1 can be spliced out)

ACTCACTGTCCCTCCCCATCTACTCACTGTCCCTCCCCATCTACTCACTGTCCTCCCATCTACTCACTGTCCTCCCCATCT

GABA-B receptor chr4:45623861-45623941

intron 7 (38 kb) 19 kb 3' of exon 7, part of 161, with some mismatch (gap in BLAT sequence)


AGGTGCAGAGCTCGGAAGGGGGCTAGGCAGTCCTCATCGTCACACCAGTAGTGCCTCATCCTCATCCCAATGGT

BMP/retinoic acid-inducible neural-specific protein (BRINP)

chr4:66089771-66089844

3' UTR?

CAACCTCAGACTCCTCATCTCTCACCCTGCTCTGAAGTGATACCCGCAGCGCAGTCCTGCCTGGCCTGTGCAG nuclear factor i (NfiB)

chr4:79723374-79723446 intron 2 (120 kb) 20 kb 2' to alternative promoter

GATAGTCACTGCATCCTAAAGTCACTGCAAGTCACTGCATCCATCAATCACTGCATCTGACAGTC

ESTs, but no good gene prediction

chr4:82968597-82968645

(misalignment)

AATCCCATTCCCATTGCTCATGAGTCTTTCTCTCCTTTTCAGTACAA

Similar to hypothetical protein DKFZp761D221

chr4:100508693-100508740

intron 1 (92 kb) 40 kb 3' of exon 1

CCTAACAGTGATGTCACTTCACCTCAGCCCCCGCCCACTCTGAAACC

LOC230541 (genescan prediction)

chr4:101409608-101409654


GGCAGTTGCAGATTTCCATTCATTTTCATGGCCATCTGGCCAACCCGCCTGCCCTTCTCCACACCTGATC

no mRNA chr4:109092192-109092261

GATGCACCACCTTCACGCAGTGCTCAGCCATCCTGATGCTTCTGCTACATCGTAGGCCACTGTCATTG

neuroglycan chr4:128360081-128360148

3' UTR 700 b 3' to stop codon

GCTGTGCCTAGGCCTGTCTGTGGCAAGCTCCTCCATCTCTCTCCCTCTGTGTGTGTCTTTGTCTCTGCATCAT


ACCACCCATGCCAGTCACCCACCCCACCCATAGTCCCAGTCACTCACCTGTATCCATGGTCGCAAGTCAC


CACCACCACCACTACCGCCACCAGCAGCACCAAACGTAATGTCTTTTTCATTTCATTGACT

patched-related protein chr4:143630924-143630983


TCCATCCTCACCCTCCACCCCCAACCCTGCTCACACAG Ubiquitination factor E4B / Ufd2

chr4:144725827-144725864

intron 23 2.5 kb 3' from exon 23

CCATCAGTTCTCTCTGTGCTCCATCAGTCCTCTCTGTGCTCCATCAGTCCTCTGTGCTCCATCAGTTCTCTCT

protein kinase C zeta chr4:150725895-150725948

(misalignment)

CTCCATCAGTCCTCTCTGTGCTCCATCAGTCCTCTCTGTGCTCCATCAGTCTCTCTGTGCTCCCTTAGTCCTC

protein kinase C zeta chr4:150725897-150725970

intron 10 (12 kb) 1 kb 5' to exon 11 (repetitive seq., some mismatch)

tcacctgtccatcacccagtcatgcatgcatgCACGCATGCACACACATTCAACCCACCCACTCATCCACCT

protein kinase C, zeta, mouse

chr4:150744198-150744237

intron 7 1.5 kb 5' to exon 8

AACCTCCATCACCACACCCCTTCCCTGATCCTAACCTCCATCACCACACCCCTTCCCCTGCCTAACCTCCATCACC

reelin chr5:20352203-20352280

intron 22 (1 kb) 300 b 3' to alternative exon 22 (misalignment)

TGCTTCTGCCTGCTTGTGCTCTGCTCCCTGTGAGCGCACGCTAATGGTCTCTCTGGGTCTGCTCTGCTTC

FLJ14026 brain protein chr5:21952686-21952755

intron 22(100b) 5b 3' to exon 23

GATCACCGCCATCACTGTTATCAGCACCGTTATCACCACCATCACTGTTATCAGCACCGTGATCACCACC

AMP-activated protein kinase (AMPK) gamma2 subunit

chr5:23553306-23553375

intron 1 (70kb) 20 kb 3' to exon 1

AGTGCGTGCTGTGGCGATCAGAGGAGGGGGATGGCTTCTCTGGAACCAGTTACAGATGCTTGTTAGCCT

actin-related protein 3-beta (ARP3b)

chr5:24244860-24244927


AGAGAGAGACGTCATCATCATCATCATTGTCATCATCGTCGTCATCGTTGTCATCATCATCATCGT

dipeptidyl aminopeptidase-like protein 6 (Dpp6)

chr5:26179962-26180026 intron 11 (12 kb) 5 kb 5' to exon 10

AGACCTTGGGGGTCCAGGTTAGTTGAGACTGCTGGTCTATGGGGTCACTCTCCTCCTCACCTTC


CTAACATAAGAGGCCCCAAGCTTCATTCACTGTTTGGGTGCGGGTGTTTGGATCCCTCTGAGTCACCTGCTTGGT

no mRNA chr5:51080989-51081063

TATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCACCCAC

KIAA0366 chr5:89463627-89463673

intron 3 (80 kb) 30 kb 3' to exon 3 (mismatch)

ACCCACCTCACTGAATCTGATGGACACTGTACAGTCGCAGTCTCTTTGTGCAGAATTGGCAGCGATGCCTGTGCTT KIAA0231

chr5:103117854-103117929 3' UTR?

ATGCGTTTGGACAGTTGTCTACATTTATCAAACGACCACCTCTGGACTCACTGCTGTTCCAGCTTCTGCA

many brain ESTs, but no good prediction

chr5:106051907-106051977

ACCATCCCTGCACCCATCTGTCCATCTGTCTGTCTTTTCACCTCTCTGTCCATCCACAGACAGGTGTTCATCT


GACCTGGGCTAGAGTCCCCCTCCCCTCATCCTCTTCTGCGTACATTCTGAACAGTCTTCTCACGGGTGT no gene prediction

chr5:114427965-114428033

TTGTCTATTCCTTAAGAGAGCCAAGAGTCCATTTTTCATCACTGGTGAATGTGTTCATCTTGGGAATCCAGGGTTCCTGGATCCTTATGAACGTCACAGTCC

protein kinase related to Raf chr5:115696483-115696584


TGTTCTGCTCATTTCATTGCCATTGCTATGGGATCACTTTATCATTGCCCCATGATGGCATCATGG calneuron 1 (Caln1)

chr5:129018132-129018197 intron 3 (100 kb)

30 kb 5' to exon 4 (alternative promoters)

GCCACAGGTCACTTGGCTTTTCTCTCTCCATGGGGAATTTTCCTCTCCTCCCTTGTATCTGTCTCCTTTCCTC

calneuron 1 (Caln1) chr5:129113412-129113484

intron 2 (20 kb) 1.5 kb 5' to exon 3 (alternative promoters)

GAACAAGACCTCATAGCTCATGAATGTCAGTGTCCTTCAGCCCACAAGCTACACAAACCTCTTACTCTGTCTCTGGGAGATATAA

autism-related protein 1 chr5:130701387-130701471


ACCAACAGTGGGAGCAGCAGCTCTCTGTTTGGCAGCTCTGCTCCATCCCCATTCACATTCGGTGGCTC

integral membrane glycoprotein

chr5:133984033-133984100

exon 11 1.5 kb big exon!

GTTTTCCCAAATCATATACCTTATACTCCACCATTCCCATTCCTTGCTCCCCC

similar to potassium channel Kv4.2

chr6:21216017-21216068


TCTTCTTCAGAATCATTTGTCTGACATCCTTGGCAATGTAGGAAAGGCTTTACCAAGTACCCTGTGAGTTCCCATCA

BF181810 cDNA chr6:36617913-36617989


ACGTCTCCACCTCACCCTCATTACTAACTTCTACCTGTGTGGTGCCCCAGGAACTGCTCTTGTGCA

diacylglycerol kinase iota (DGKi)

chr6:37138991-37139056 intron 20 (40 kb) 20 kb 3' of exon 20

ATGACGCAGGTGCCACAGCTCCTGTCACCTCCCTCGGCGCCAGCATATGCGCAGGAAGAGCAC

diacylglycerol (DAG) kinase chr6:37184474-37184536


CAATCCGTCTTACCTGTGTTCACAGGCTTGTCAGCACTCCTGGGAGACCCACTCTCTCCCTGTAG

cDNA clone chr6:38084282-38084346

intron 12 kb 5' to intron?

TTACAGATTTCTTTGTTCCTTCTCCGCTCCCACTGCTTCACTTGACCAGCCT

Y3 scRNA chr6:48109705-48109756

TTCCTGTCTCATCCCTGTGCACTCCTGCACACTGTGGCCTTCCCGTCTCATCCCTGTGCACTCCTGTACACTGTGGCCTTCCCGTCTCATCCC

PALS2-alpha splice variant chr6:50574032-50574124

intron 11 200 bp downstream exon 11

TGACTGGGAACCCATGTGATCAGGCACAGACTTTCCTCATCTTTCTACCAACCACTCCAAGTCAGTC

RIKEN cDNA chr6:83532629-83532695

3' UTR

CAAGCGAACCCAGGTCAACTCATCACAGGTCACCGGCTGGGTCTTGGGGTCGCTGGCACAGCTGATGGCCTGCTT

(STAR) steroidogenic acute regulatory protein

chr6:84658989-84659063

3' UTR

TCTAGAATGTTCATTGCTCATTGGTTTTCTTGCTGTGTAGTCCAGGCTGGCTGAAACCTGAGGCCTTTCCTCCT

Hirip5 chr6:87876871-87876944


TCTACACCTCCAACATCCCCATCATCTTGCAGTCTGCTCTGGTGTCCAAC

Sec61 alpha subunit 2 chr6:89376214-89376263

exon 9 881-930 (stop codon 1461

CAGCTCTCAACATTCAGTAGGCATGCTAGGTGTGCTCTCTCATTGGCTTTCGAAGTAAGCTCAGCC


ATCATCCAGGCTCCTGTTCCTGTCTGTACTCACCCCCAATTTGCCTAAACCCCCCCCCCCAAAT

mouse contactin 3 chr6:103365191-103365255

3’ UTR


ACTCCATCCTTCACTCTCTCCCTCCTCACAATCGCTCCTCCTCGCTCTCAGCCTGGCCCCCCAGCCCTCCTC

plasma membrane Ca2+-ATPase 2 (Pmca2)

chr6:114658986-114659058

3' UTR

AACTCCATCCTTCTCTCTCCCTCCTCACAATCGCTCCTCCTCGCTCTTC

ATPase, Ca++ transporting, plasma membrane 2

chr6:114659009-114659059

3' UTR

GCTCATCTCGAGGACCATGATGAAGAACATCCTGGGCCACGCCGTCTACCAGCTCACCCTCATCTTCACCCT

plasma membrane Ca2+-ATPase 2 (Pmca2)

chr6:114673868-114673939

exon 13

AACGGCACTTTGGGCTGAAAAGGTTCTTACTGCTTTTTATCTACTGGCACTTTTTCAATTAAGGAGTCTCCTCTGAGATGATCTATCACCTCCCTGTCTG

L-type calcium channel alpha-1

chr6:119697452-119697551


AGAGTACCGGGATGTCTCTGTTACCTGGTAGAGGTTCCCGATGTCATTCATCTGTCTGTCTCTGCATCAGCTGACCA


last intron 50 b 5' to terminal exon

GTCATTCATCTGTCTGTCTCTGCATCAGCTGACCATCTTCCAGTGGTACCTCTCCTCCCCTGCTCACCCCTCAC


intron /terminal exon junction

CTTCCTTCTCTGTCCCTTCTCTACCCATCCCCCTCCTCCATTTGTCCATGGT

brain ESTs chr6:12499437-12499488

CCACCGGTCCAGCTCCTGACCCGCCTCATCTGAGCTCCCCAGCCAGCCCTCACTTGCCCT 11.5 kDa Zn-binding protein

chr6:125801027-125801086 3' UTR 220 b 3' to stop codon

CCTTCACCCTCACTGCCACCGGTCCAGCTCCTGACCCGCCTCATCTGAGCTCCCCAGCCAGCCCTCACT 11.5 kDa Zn-binding protein

chr6:125801033-125801101 3' UTR 200 b 3' to stop codon

ACAAATCCAGCCCCCTTTCTCCTGGCTCCCTGCTCTGGCCCTGCCCCAGAGCTGTGACCCTTGTCCTTTGACCCAGCCTCTCATTTCCATCTCTC

11.5 kDa Zn-binding protein (parathymosin homologue)

chr6:125801113-125801207


AAGTGTATGGCAGTCCCATTTTTCGTCATCCCCATCCCATTTCTGAGCTGTGCTTGCGCACTGGGTCTTT

N-methyl-D-aspartate (NMDA) receptor subunit NR3

chr6:136477292-136477361


TAGACCTGGCTTCGGTTTCTACCTCCCCAGTGCTGTCATGTTCATGTTTGTTTT

homolog to ETHANOLAMINE KINASE

chr6:143792762-143792815

3' UTR 1.5 kb 3' to stop codon

CCCTCATTGCTTTCCTCATCGGCCACCTGCAGTTGCAGGTTTCCTCCCACTGTTCTGGCCTCACCACTCCTG KIAA1932 brain protein

chr7:3475872-3475943 exon alternatively spliced part

TCCATTTGTGCATCAGACCCATTACCCACGGCCCTTCTCACCCCTTGCTCATCAGCATCACTTGATGTCCCTT

Na-Ca exchanger NCX2 isoform

chr7:11292341-11292414

3' UTR

CATCTGCCACTAATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCGTCTGTCCATCTGTCCATTCATCCTTA no gene prediction

chr7:113883060-113883138 part of (TCCA)n repeat

CCATAGACGGGCCCATACTGCCAACCCATTGCACCGCTGTCGCTGTGGCAAGACCTTCAGCAACATGAC

(XM_057401) similar to Zinc finger protein 84

chr7:17468841-17468909

exon 3

AGCTGACCACCACCCACCATCCATCTCCATCCCTCACCACCGCC

N-acetylgalactosamine-4-O-sulfotransferase

chr7:25184937-25184978

intron 2 (53 kb) 26 kb from exon 3

ATCCACCCACCCACTCATTATTCACCC Shank1 ~chr7:33890068 intron 7 200 b downstream of exon 7CCTGGTCCCATGCTGCAGACACACATGGGACTTTCCTTCCCTCTCCTGCTCC

Shank1 chr7:33924680-33924731

3' UTR

CTTCTGTCCCTCCATCTGCGTCTGGCCCCCCCCTCTGCCGCTGCTATCATCACCAGAAAT

synaptotagmin 3 chr7:33966903-33966965

3' UTR 415 b 3' to stop codon (3 b misalignment of CLIP tag)

GATGAGCAACACTCACCATCTTTCGTTTGAGTCTCACGACTGTGAGATCAACCCATGCACCGCTCTGAGA

ribosomal protein L13a chr7:34694154-34694223

intron 2 (300 b) 50 b 3' to exon 2

TCCATGATGAGCAACACTCACCATCTTTCGTTTGAGTCTCACGACTGTGAGATCAACCCATGCACCGCTCTGA

ribosomal protein L13a chr7:34694156-34694228

intron 2 (200 b) 30 b 3' to exon 2

AGCGGCTGGGTTGCTTCTGTTTTTGTCATCGTCATCATCATCACCACCATCACCATCACCATCATCATTG

SGP prediction chr7:38817115-38817184


CATCAGTCAGCCAGCTTATTTTGAGGAGGTTTTTGGATTTGAAATCAGCAAGGTTGGCATGTTGTCTGCAGTCCCTCACCTTG

vesicular glutamate transporter 2

chr7:41282907-41287435

exon 8-9 junction

TCCATCTATGGGTGCTGTGAAGCCATTTTTACAGAAGCCATTTCATGTCCCGATGGCAGCATTTGTGAGCGC no gene prediction

chr7:49342267-49342338

ACCACCACCAAGCCTGCTGCTGTCAAGCCAAGGACTATCGCTGCTGGGACTCATTGGAGCTCCCCTTCCCC

? chr7:51295705-51295775

intron (15 kb) 5 kb 5' to exon ?

TCTCCACATTATCCCTCTGGAGCTCGGGTGACAGGCCTCATCAGGTTCACCTTCTGCGGCTTGTGGTCACA

FLJ10010 (brain protein) chr7:59844258-59844329


TAATGTCCTCTTTCTAGGCTCCACCCAGCCATGGCTGCTACTTCCTATTAGAGCCACAGCCCATGCCTTTGGCATATTGTCTTTAGGGACTTTGGGATCTACATCATAATGTTGTCATGGAAAGGGTTTCCTTGTCTTGTGTTTCCCTCTTCTTTCTTTTCTTGACGCATGAGTCTTTCTGGACTCCTTTTAATGTCCTTTT

neurotrophin-3 receptor non-catalytic isoform 2 (trkC)

chr7:67923824-67924025


GGACGGAGTCAGCGGATGCTCTGTACACCTCTGGCTCATCTGTTTCTCCTCATTTCTCCCAC

chapsyn-110 (channel associated protein of synapse)

chr7:82193504-82193567

3' UTR

AATGGCTGCATCATGTCAGAAGGCACTGTTTCACAGCAGGCCTCCCTAGCTGCTGTCTCTATGACGTTCC no gene

chr7:100183344-100183413 part of Lx8, L1 LINE repeat

TTCTACCATCCCCTCCCCTCCCCACCCCATCCA translation repressor NAT1chr7:100674353-100674385 exon 2

GGCCCACCTCTCACCTTCTGGCTGAAGTCCCATTTTCAGACCAAAACCTGTGGCCTTGTTGGTAGGAA


CATCTGCCACTAATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCGTCTGTCCATCTGTCCATTCATCCTTA


ACCAGTCCTAGCCCCGTCCCCAACCCCTTTCCCTTGGGGAGTTGGGGGAATTCCTGCCAA

ataxin-2 related protein chr7:116347188-116347247

3' UTR

AACTCCAGCCTCATCGATCCAGCGCACTCTGCTGGACCCTGTGGGCACACATTCTCATATACA

meltrin alpha chr7:124083249-124083311


TTGCCACCTTATCATCCTCATTTCCATCCTTGTCGGCTGCCAACCTGCTCATCGTCACCGGGACCTTCG

solute carrier family 25 (mitochondrial carrier)

chr7:131744322-131744390

exon 3

TACAAACCTAGATGTCCTTACCACATCCGGGTCCTTCCGACCCACCTCGAGATGAACATCAT

Csmd1 / hypothetical protein XP_163816 (genscan)

chr8:17437171-17437233


GCTTCCCATCCGAGTTTCCATCCTCACACCTGCCCACTCACCTTCCATGTCGCTATCTGTGTCCCTC


3' UTR of AB060832?

CAGGGCCTTCTTTCCCGTGTCAGCACTTGGATGCCAGATTTCCCAGCCTC

glutathione reductase chr8:32575577-32575626


AGCATATCTGGCTGTCTGTCCCTTCACCCATGCACCCAGACCTCACATGTGTGCCAGCCTTCATCCTGT

TRF1-interacting ankyrin-related ADP-ribose

chr8:33751977-33752045

3' UTR

ACATCTCCATGTTTGCAAAGCAAGCCCTCTAACTCACCGATCCATCTCCCACAGCCCCTTTGCTCA no gene prediction

chr8:37422342-37422407 part of B4A SINE repeat

TTCATTCCAGAGGGGAAACATCACCCTGCTGGCCTCTGCTCCCCATGACCCC

epidermal growth factor receptor pathway substrate 15, related sequence

chr8:71770514-71770565

intron 3 200 bp from exon 3


ACTGTAGCACTGTGAGCTTGTATGTGTAACCGTCCTGTGGTGTCCAGAAGTCACTGTCTTGTTGCATTCGTCT

inositol polyphosphate 4-phosphatase type

chr8:81165453-81165525

intron 1 (300kb) 80kb 3' to exon 2

ATGCAGCTGCCTACATCCAAACACAGTTTGAAAGCAAAAACCGCTCACCCAACAAAGAAATTTACTGTCACATGACTTGTGCCA

guanine nucleotide binding protein, alpha o (Gnao)

chr8:93751770-93751853

3' UTR same as Kirk's

AGACTGGGTTACATGGAAGCTGGGCTCTCCTCCATCTCCCTCCCTCCCCCTCTCTTCCCCTGTCTGAAACA BC021949

chr8:94628079-94628149 3' UTR

CAGGGGCTCTAACCTATCATGGCAGAACAGCCCATTCATGGTGGTGGAAGCTGTCACATCATAGCTACCCAGGCAGTGGCAAGGCA

zinc finger, DHHC domain containing 1 (ZDHHC1)

chr8:105330401-105330487

alternative exon 3 exon 3 & 4 alternatively spliced

CATCATCTCCTGCCCAGACCCCAGCATCATCAGCATCAGCATCATCTCCTGCC

BB529891 cDNA = hypothetical protein XP_150136

chr8:105474366-105474418

intron (12 kb) 5.5 kb 5' to exon

AAGGTGTGTCATCACATGCAGCACTCATGCTTCTGTCTCCAGTGATGCCCGTCCGGCTGAAGT

cytochrome b5 chr8:107024663-107024725

3' UTR? (prediction on basis of m-h homology)

CTTGTCCCCACACCTCTACCCACGGTCATCTGCCACCTCCACCATCTATCTCG

KIAA1923 WD repeat protein chr8:111377449-111377501

intron 26 200 b 3' to alternative exon 26

CTGGCTTGTCCTCCCCAGTTCCTTCCTGTTCATCCTTCGCACAACTCTGACTGCCCACAGCCCATGCTCCATGGTGGCTAAGTCCCATGGTGCCAGATGCTGACC

KIAA1923 WD repeat protein chr8:111415997-111416102


CCAGCCCTCAGTCGTTCTGTCGGGTCCTGTACACTGCTGTGGTTTCTCACTTCCCAGCCCTCAGTCATTCTG

BCNT chr8:111741651-111741722


ATGCACTTTCCCATCATCTGTCCACTCACCTCCCCCACCCATCCATTCACCCATCCATCCATCCACCCACCCACCCATCCATCTACCCACCCATCTATCTACTCACCCATTCA

KIAA1694 chr8:117328345-117328457


CAGGTTTAGGCCTGACTGTCTGTCTGTCCATCTACCCATTTGTCCTCAATTCACCATCCTTCCATCCATCATCTC H/T-cadherin

chr8:118530091-118530165 intron 2 (160 kb) 25 kb 3' of exon 2

AGCTCACCATCCTCCCAGCTCACCATCCTCCCAGCTCACCATCCTCCCAGCTCACCATCCTCCCAGCTCACCAT H/T-cadherin

chr8:118886807-118886880


CAGCAGTGCCCCGGCTCTCACACGCACAGCACTCCCCGCCCTGCCCCACCTCTCTTAGAAC

solute carrier family 7 (cationic amino acid transporter, y+ system), member 5

chr8:121953545-121953659


GCTATGGCCACACGGTGCCCCTGTCAGATGGGGGCAAAGCCTCTGCATCATCTACTCTGTC

TWIK-1 K+ channel chr8:126032561-126032622

exon 2

AACCTCATCCATGCTAACCTCATCCATGCTAACCTCATCCATGCTAACCTCATCCATGCTAACCTCACCCATGCC

5-azacytidine induced gene 2 chr9:119292706-119292885

intron 4 (1.4 kb) 500 b 3' to alternative exon 5

TAAATATATTATTCTCATTTAGTGCCCCTGTAGCCAGAACCTCATTACTGCTTCATTTTTGTAATAACATTTAATTTAGATATTTTCCATATATTGGCCCTGCTA

CDC10 chr9:25398787-25398891


ATGGGAAGGGGGCCCTTCCTCCTTTTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTGTCACTCATCCCC

neural cell adhesion molecule (NCAM)

chr9:49898505-49898573


TCCTCTTCCATTCACGAGAACGACAGGATTCGATTCCAGGCCTTTCCTTAGTTCTCTTAGAACCCTCATCTCTCTCTA

secretory carrier membrane protein 5

chr9:57977035-57977112


CTGTGATTAGTGCCCATCCCATCCATTCCCTCGATAACCCTCACCATCATTTCCACTCCAG

neogenin chr9:59424988-59425048

alternative exon 23

AAAGCGTCTGTGTTTATTAGCCTTGTGTGTCACTCATG DDM36 chr9:65715954-65715991

3' UTR

TCAACACCACAGGCTGACCCCTGTCCCTTCTATATTTGCTGCATATGTTCA

ubiquitin specific protease 3 (USP3)

chr9:67172147-67172197

intron 1 (26 kb) 12kb 5' to exon 2 (misalignment)

TGCTGGGTTGGTACTTAACCTCTCCGGGTACCGGATGGAGGTGTACTGTTCTTTCAGAGGCTCGGGAAGGAATGAAACTTTAAGTCACTCAGATTCTATGTCCCGTCAGCAAGTGGGTGACACGAATGTCCTGTTATGCTTGAAAACCCTCCTGTGATTGGAGAGTT

nuclear orphan receptor ROR-alpha 4

chr9:69895008-69895174


CCACCCCTCCCCTTCACCTCTGAGAAGGGGGAGGTCCCCCTCTGTATCACCCCACCCTGGCACCTCA KIAA1164 brain protein


CCATTTCTGCCATTGCTCTAAAATGACTTCACTCCTTCTCCAACTCTGCTTTTGTTTACACTCCTGTGCTTCAGTAACACCTTG


CCTGACTAAGACAGTCACCCAAGCTTGTATGACGTGGAGTTGAAGTTCATGCTCACTTTTGTCTT

protein tyrosine kinase(NET PTK)


AATTCCATTTCATTGTTCATCCTCAAAAGTCAGGGCAATCAAAGCAGAAA

clone MGC:3040 (brain neuroblastoma protein)

chr9:104465359-104465408


ACATCTGGATCCTCCTCACACCCACATCTGCATGCTCCTCACACCCACATCTGCATGCTCCTCACACCCACA

ARPP21/TARPP chr9:113217776-113217847


AATTCCTCATCCTCATTGCTTCCTCCTCACACCTACATCTGCATC

ARPP21/TARPP chr9:113217929-113217973


TTCACCATTTCACATGTTTGTACTTCTTTGTCTTCCCATTAACCTTTGCCAGTGTTATGATTGTATACATTTTTAAAAATGCTGGTTA

CLASP2 chr9:115040743-115040830

3' UTR (exon 16) 250 b 3' of stop codon

TCAGCATCCAGCTGCTTGNTGTGTGTTAGTTGTCTCACAGCTGAGGGCTCTGCCTCGGCTACTTCAGGCTC

FLJ20396 - chemokine-like factor super family 6

chr9:115941885-115941954

3' UTR

CCACATTTCAGTTCGTCTCCATTCACTGCCTTGCTCATCCATCACGCATGCTTCAGTGTGGCGGTGGCACCCT phospholipase C delta-1

chr9:120330255-120330327 intron 1 (40 kb) 10 kb 5' to alternative promoter

GGAACTGATCCCCCTCTTCTGGCCTCTACAGGAACCATACATGCTCATGGTGTG

genescan prediction (homolofous to synaptic nuclei expressed gene 2)

chr10:5176401-5176454


TGACAAGCTGCTATTCTCTAAAACTCTTGAAATTCATAGTTTCTGAATAGAAGCAGGCCTGGTGTCCTGCTGTGTG

AV244488 head EST chr10:32737611-32737682

intron (250 kb) 120 kb 3' of exon

CATTCCACGACACAGTTCTGACTCTCCGGGTGACTGTCACCTGCTCCCATCCTCTTCTTCCTCCCTCCCTTCCTCA KIAA0275 brain protein

chr10:60118469-60118544 3' UTR

AAAGCCATTACCTCCCCTCTTCAGCTCACTGCACCCTCTGTTTCTGGGCGTCCAGAGCAGTCTGTTCTCTTC

DNA binding protein DESRT (Desrt) / MRF 2

chr10:68169667-68169738


ATTGGCCAGCCCTCATGGCCATATTTTCAAGCTCACCTACCCCATGGCATCTCTCCTCTCTCCACCTTCTTCCTTC

bcr (breakpoint cluster region)

chr10:75532521-75532596

intron 4 (4kb) 2 kb (3' of exon 4)

AAACCCTTTCTGCCAGGTGACCACACGCAGCTTCCCTGCCCGCTCCTTCATCACCTTCCG

Flamingo 1 chr10:76349740-76349809

exon 4 4093-4145 (stop codon: 8763) (ccc.ttct)

TCTGAGAGGGGGCTTCATTCACCCAGCCCCACACCTCATCCATCTAGCATGCATCCTCCTTCCCTGGGGCATC

E2a-Pbx1-associated protein (EB-1)

chr10:90482197-90482268



CCACCATCACCACCACTACCACCACCACCACCATCATCATCATCATATTTCTGAGACAGGATCTCAGCA no gene prediction

chr10:110230382-110230450 part of (TGG)n repeat

TTTATCCATACAAATCCCTCCTGCTGCTCGTCATGGTTGCTG

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2

chr10:129153689-129153730

intron 27 300 bp downstream of exon 27

TGGGATACCTGCCGTGCTGTACACATTCATCAAACTGTTTGCCCAGAGGAAGGAAGGGGTGAGCAGGTCA

uridindiphosphoglucosepyrophosphorylase 2 (Ugp2)

chr11:21339071-21339141

3' UTR

CAATCTCTGCATGGACTTTCCTTCAGTCTCTGCTCCACACTTTGTCTATGCATTTCCTCCCTTGAGTA



TTCTCGCTCGCCCATTTGATCGCAGCTTGAGGCTGCACATACCCTGCATTCTCCTGCGCAC BB653452 brain EST

chr11:29935096-29935156 intron (120 kb) 30 kb 5' to exon

CAAACCATCATCATCCTAAACAACCGCAAATTTGCTAATTCACTGGTTGGGGTCCAGCAGCAGCTCCAGGCA

brain beta spectrin (Spnb-2) chr11:30111273-30111344

exon 7

AATTCCACACTCCTGTCCATTCCAGGGAGTGACCACTATCAGGAATCTACCTCCATTTCCTATAGGCACTTTACCTGGATTTTC

Teneurin 2 /Neurestin alpha chr11:37118813-37118897

intron 3 (470 kb) 60.5 kb 3' to exon 2 (two alternative promoters 120 kb and 300 kb downstream)

AGGCCACATTCATTGCATATACTTTCAGCAGAAGCTGAAACCACAGGTGAACTCGCAATGCCCGGT

Teneurin 2/neurestin alpha chr11:37233999-37234064

intron 1 (80 kb) 20 kb 3' of exon 1 (alternative promoters dwonstream)

GAGTGGCTAATCATCTCTGCGGGCAAACTGACAGTACATCCTCTAGAATTCCTTCCTTCTCATTTC

early B-cell transcription factor

chr11:45203604-45203670


GTGTTCTTCCATTTTCCACATTCTTCACGCTAACATGCGTCTTCATGCT

JNK/SAPK alpha (JNK2) chr11:50285204-50285252

intron 6 700 bp downstream of alternatively spliced exon 6

TGTGGCAGCCCACCGCTCACTCACTGCCACAGCAGCAGGGAGAAGATCGTCATCCCCTTCTTCAGTCTGCTCATCA

AB060868brain protein

chr11:50381111-50382254

exon 9/10 junction

AACTCTGAGGCCATGGCCCATCCACAGCCTCCTGGTCCCCTGCACTACCCAGTGTCTCACTGGCTGTGTTGGAAACGGAGTTGCATAAGCTCACCGTCCACAAGCA

SPARC-like 1 (mast9, hevin) chr11:55880407-55880512


ACTGAGACCCCGGCGTTGAGCTGCCATTGTGGCATCATGTCACATCATATTGTCATCTTTTCACCA

brain protein chr11:59945339-59945407

3' UTR

CCAAACATTCAAACACATGAGTCTATGGGGGTCATTTCTATTCAAACCACCAACACCCTGCTTCTCTCCACCTAC

axonemal dynein heavy chain 9

chr11:66538213-66538287


GTGGCAAGGATATATATGTCTGTGCCTGTGCACATGCATTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT

rabaptin-5 chr11:71461782-71461854

intron 2 (27 kb) 12 kb 3' of alternative exon 2

TCCATGACCATTTCATTCCCTCTTCTAAGTGAGGCTCAAGCATTTTTGCTTGTACCCTCCTTCCTG

rabaptin-5 chr11:71493024-71493089

intron 4 (6.4 kb) 3 kb 3' to exon 4 (exon 5 absent from delta isoform)

TCATTCATTCATTCATTCATTCATTCATTCATTCATCTTTTTCTGT

rabaptin 5 chr11:71535096-71535144

intron 13 2200 b 5’ of exon 14

TCAGACTCAAAGATTCATCTGCCTGCTTCTGCCTCCCAATTGCTGGGACTAGAGGTGTGCAGCTCCACCACCTG

hypothetical protein XP_109700

chr11:105177642-105177705


CATCCATCCATCTACCCATCCATCCTCTTACCCATCCACCCATCCATCCATCCA


CATCTTCATCTACGCGGCCATCGCCTCTCCATCACCTCCTGCATCTTCACCTATATCCATTTGCA

UGS148 chr11:71635810-71635875

exon 1 344-409, stop codon: 419

GTCACCATCTTCATCTTCATCATCATCATCTACTGGGGAAACTCAGACCCAGTCTTCAAGTCGGTTATCCCAGGTCCCGATGTCAGCTCTGAAATCTGTTACTTCTGCCAGTTTTTCTAATGGGC

KIAA1321 protein chr11:78326336-78326460

exon 2 (1713 b long!!!)

ACTCACAGAATTCCGNCTGCTTCTGCCTCCGGTCCCATTTCTGGGATCGACGTGTGCTACTACGCCTG

PHD zinc finger transcription factor

chr11:78617928-78617995

3' UTR (no gene prediction)

AATCCAGCCATTCCAAACACCCCCACCCTGGTCCCTGATCATCAC

SARM chr11:79111832-79111876

(exon/intron junction)

AACCTCATGGTCCACCATCCACCCATCCATCAGTTCACCCATCCATCCATTCACCTAAGCACCCACCATCAA

brain sodium channel 1 alpha subunit (Accn1)

chr11:81574052-81574123 intron 3 (60 kb)

30 kb 3' to exon 3 (misalignment)

ACCTCCTCACCCTCTCACCTCCTCACCCACTCACCCCCTCACCCACTCACCC

brain sodium channel 1 alpha subunit (Accn1)

chr11:81595014-81595065

intron 4 (60 kb) 7 kb 3' of exon 3 (alternative promoter in intron 1)

TGCCTCCTGCCATTGATGATCGTTCTTCCCTCCTTTGGGAGGGTGAGAGGGAGGGAACGCAGTCTGAGTGGA


TGGGAATGGGGAGCAGACTCGTCTTGCCGTCTGTCAGGATRhoGDI-1 chr11:88646905-

886469443' UTR

CATCATGCCATTCCTCTCAGTGACACAGGTCAGGGTGTCATCCCACTCTTCTTAATGATTTGGTCAGGTCATCA

Carbonic anhydrase-related protein 10

chr11:93890855-93890928


TCTCCAAGCCTCAGTTTCTCCAGGCCACCTCCTGTCCCTCCACCCCTTGTTTGGTTGAAC

voltage-gated calcium channel, alpha-1-G

chr11:95210325-95210384


ACCCAGCAGGGGGCAGTGTGATGCCGGCCACGTCATCCCTCCCGCTGTCCTTGTCTCCATTCAT

ADAM11 (disintegrin) chr11:103563305-103563365

alternative exon 26/intron 26

within 3' UTR of shorter isoform?

TCTGTGTCCATTTGCCCATGTCTGTCTGTCTGCTGCTGAGGCAGTCATCCATCTCGTGTCCCCNTCTGTGTCGTGCTAGCACTTAAGTGGGAACAAA

WD-repeat protein chr11:106839035-106839131

3' UTR

TGCACCCATGTCAGGCATTTCACAACCACCTGTAATTCCAGCTTTCCTTGCCTCTGTGAGCATCTGCACTC

E3 ubiquitin ligase Smurf2 chr11:107674857-107674927

intron 1 (45 kb) 10 kb 5' tp exon 2

GAAAGTCATGTTCACGCTGTGCCAGCACTGGCCTCCTGCCTCTGCTCAGCCC

KIAA1917 protein chr11:117239622-117239674

intron 1.3 kb 3' to exon

AACAAGCAGCTGGCTCGTTCTGCGCAATCTCACACCCCAGATCGATGGTTCTACACTTCGGACGCTGTGTCTGCAGCATG KIAA1582 protein

chr11:118668079-118668807 exon 16/17 junction

GTGTCTGTGCACATCATTGAGGGTGACCACCGCACACTGCTGGAGGGCAGTGGCCTGGAATCCATCATCAACATCATCC fatty acid synthase

chr11:121745149-121745227 3' UTR

AACTCATCGTTTCTGTGGCTTGGCTTGTGCCGCTCACTCTGTCTAGACTTCATCTCATTTCCTCTGTGTTCAG

B-cell receptor-associated protein 29

chr12:25732175-25732249

intron 1 (3.3 kb) 1.3 kb 5' to exon 2

CCCCCATCCCATTGCCTGCTTCTATGACAGTGCTCCCTCACCCACTCCCATATCCC

no good gene predicted chr12:39922265-39922321

(part of Lx2, L1, LINE repeat element)

AAACATCAAAACTCCTATCCTCGCGCCAGGGCTGACCTCATCTTGTTCCACCCCATCTCATCCAATCAG


GTTATCCTGCTGCCATTTCCCTTCCCCCCCCTCTCCCACAAAGATCCCTCCCTCCTTCTGCCTCCCATGAT


part of LINE repeat

CCAGTTCAACCACAGGTCCCCAGCTTCCATCCATTGGTTGGGTGCTAGTATCTGCATCTGACTCTTTCAGCT

gephyrin chr12:73163177-73163248

intron 6 (10 kb) 2 kb 3' to exon 6 (exons 4 and 7 are alternatively spliced)

CCAACCACAAATGCCAGCACCTCTTAATAACAATCAGCATGACCTCTGCCTAAGTCTTGGCTTCTTCCTCAGAA

gephyrin chr12:73256858-73256931



GTTGGTCACAAGCCATTGGGATGTGCCTGTCTCTGCCTACTCCAGTTCTGGATTACTGGCTCACACTGCCACACT

BC005675 chr12:76112833-76112907


GGATCAGAAACACTCTCCTCCACTTCCAAGTCACCATGCCCACCTTGGT

secretory protein containing EGF domain

chr12:81794544-81794592

?

ACGCACATCACTGTTGTGATGCAGTGAGCTGCTCCTTTCCTTTATCTGCCTCTCGTTTCCAGTCATCCC

neurexin III-alpha chr12:83614745-83614813


TCAGCATACACAGAGACACGCAACATCCAGTGCAAGCTGGATTTCCCACCAGGTTCTCTAGCCACAACTCCTGAAAC

calmodulin 1 (phosphorylase kinase, delta)

chr12:94384120-94384196

3' UTR of longer isoform 70 bp downstream of shorter isoform

TGCCTCCTCATCTCAGCCTCACCATCTTCACCTGCTTCATCTCAGCA

no prediction chr12:103051773-103051819

TGACCCTTGGCACAATGCCAGCTCTGGCTGGACACAAGGACACACGCATCTCCTCCATTCCTGCTGCTCCATTG

Gtl2 chr12:103806757-103806830

intron 8 (2.6 kb) 20 b 3' to exon 9

ACTCAGAGCAGGGGGAAGAAACACACCCTCAACTCTGCTTCCCCGTGCTCCATCTTCCTTTCTGCCTTCCA

Gtl2 chr12:103824624-103824694


GCCTGTGTTCAGCCCTCTCACCCCATGCTTATCTGGACATTGAAGCTTGGAAAGCCAGTGGTGACTTC

Gtl2 chr12:103826302-103826369


TGTGTTCAGCCCTCTCACCCCATGCTTATCTGGACATTGAAGCTTGGAAAGCCAGTGGTGACTTCAACT

Gtl2 chr12:103826305-103826373


TCCACCCATCCATCTGGCTATCCATCTAGCCATCTGTCAGTCAATCCATCCATCCATCCATCCATCCATTCATCCA

Gtl2 chr12:103826387-103826462


AGCCATCTGTCAGTCAATCCATCCATCCATCCATCCATTCATCCATCC

Gtl2 chr12:103826414-103826455


AGCCATCTGTCAGTCAATCCATCCATCCATCCATCCATTCATCCATCCATCCATGCAT

Gtl2 chr12:103826414-103826465


CCATCTCAGTCAATCCATCCATCCATCCATCCATTCATCCATCCATCCATGCATACACACATTGGGCCTCCATCACTTGACCTGGTGCT

Gtl2 chr12:103826416-103826510


TCATGAAGCAAGGCCCCCATTCACAGCCTCCTCCTCCTCCTCCTAGGTCACGGCTCTGAGCACGTCCCAGCTGGACCCCTATCACC

Gtl2chr12:103826583-103826668 intron 13 4.6 kb 5' to exon 14

GGCTTCCCACACCCCACACCCTCCTCCTGTGATCCAGGAGGGCCAGATTCCCAGAGTGCCCTGGGGCTGGCCCTTCCCAC

Gtl2 chr12:103826687-103826766


GCGGAGCTGCCTCCCCAGGCTTCACACTGCCTGGTGCATGGTCCCTCATGAGCTTGGCCTTC

Gtl2 chr12:103826772-103826835


AAGTCTGTCTAAACACCAGATCGCATTTGTGACTCATTAGCATTTCTCATCCCACCAACGCCTGCCTTTCCCACTCACTTTCCCC

no gene chr12:103926771-103926855

GAATAGAGGCATCAAGTCACGATGTTGTCAGTGGGAAGCAGCTAGGTCTGCCCTGAGGGTGGTTTCCAGCTTTG



GGATTCTCACCTTTCCCCCTGTATGTTCTATACCTTCTCTTCTTCTTTCCTCTCTCTCATCCTCTCCTTCCCTT



ACTGCCTCCATGCATCCATCCATGATCCATCTGTCTTTCCATCCATCCATCCATCCATCCATCCATCCATCCATGCATACAC

cardiac ryanodine receptor 2 chr13:11711606-11711675

intron (1.5 kb) 400 b 3' to exon

ACTTCATTCCATGATCACAGTTACCATACTGTCACTGTCACACTCACCGTCACACTC

no gene chr13:23529735-23529791

(ATGGTG)n simple repeat

CCACCTCCACCTCCTCCTCCCCTCCCCCCAGGGCTTGCCTTCTATGGAACAGATATCCCACCCATCAGTG


intron 11 400 b 5' to exon 12 (alternative exon 11)

GTCTGTATCTCTGTCTTCTCCATCTGTCATTTAGCCACCAATCCATCTTT

RIKEN cDNA chr13:28954184-28954233

intron 3 (31 kb) 800 b 3' of exon 3

TGGGGCTGCCCCTGCCGTAGCCCAGCTCAACCCTCAGCCGGCTGCCAGGATTTCTTCCTCAGTCTCACCTCACCC

zinc finger protein alphaA-CRYBP1

chr13:41760053-41760128

3' UTR

GCTTAAGTCATTAGCGGGGTCATCGTCATCATCACCATCATCACCATCGCCATCATCACCTTCTTCATCATCG

KIAA1733 protein chr13:42526026-42526098

intron 3 (250kb) 10 kb 5' to exon 3 (alternative exon 2?)

TCCATCCATCCATCATCCACCCATCCATCTATCCATCCATCCTCCCATCCATCCATCCATCCATCC ataxin-1 (sca1)

chr13:45282390-45282455 intron 7 (120 kb) 10 kb 3' to alternative exon 7

CCAGCTTGCAATCCCACCAGCAATGGAGGAGTGTTCCTCTTTCTCCACATCCTCACCAACATCTGCTGTCA no gene

chr13:72590456-72590526

AAGTGGCAGATTCACGTCCCAGGGTTCAGAGGTGGCAAACTTCTCAGTGGCAGCTGTGCTCGGTCATGC

MAP1B microtubule-associated protein

chr13:96780336-96780404

3' UTR

AGATTTCGAGTTACTGCAAAATTGCCTACCCCCGTTCATCTCTGCTGAACATTCGG

MAP1b chr13:96782250-96782305


TACATAGTCAGGGGAGGGCCCCTGTCAACGTGCCCACAAGGTTCCTTTATCCTTTGTCATTACGTCATTGTCCAAGGTGACAGGAGGAACTCAGTCGTTAAAATGACGAGCCTTATTTTCATGA

MAP1B chr13:96859716-96859839

intron 2 5 kb 3' to exon 2 (alternatively spliced exon 3) 64 kb intron

GTCTGTCTGNCTGNCTATCTATCTGNCCATCCATCTATCATCCTTCCCTGCCTCCTTCCCTTAACCCGCCCCCCCTCCATCAGCC

cDNA AW455876 / Genie Gene Prediction

chr13:98063460-98063544

intron 1.5 kb 3' to exon

TTGTCATCCTCAATATCACCTGCACTACGCTTCTTAAGTTTACTATTGTCATCC

cyclic AMP specific phosphodiesterase PDE4D5A

chr13:107219572-107219624


GTCTACAATGCATCCCTACCCACTCCTATCCCATCTCTGcttgtggtagttagtgtactatcaccctcat ttct

small GTP-binding protein Rab3C

chr13:107624228-107624266


GAATCTGTCTCCCCATCATCTATCACATGAATCACAGAATCTGTCTCCCCATCATCTATCACATGAATCACAGAATCTGTCTCCCCATCATCTATCACATGAATCACAGAATCTGTCTCCCCATCATCTATCAC

actin-binding protein homolog ABP-278

chr14:3154768-3154901


TCGTTCAACTCTTCTCATTCAAGTTAGCAGTCATTTCAATCAGTTCAATAAGCATATTAGGCAAGCA

neuregulin-3 (NRG3) chr14:34400062-34400128


AGGCGTGGGGGATCAGGGTCTTAGACTCTGCCCCCCCTCACCCCACTCTCTTCCCATGTTCGTTGAT

KIAA0323 brain protein (HCDI)

chr14:46995006-46995061

intron 6 100 kb 3' to exon 6 (ESTs show a lot of alternative splicing

CTCAAGTCAAGGACAGTGTAGGTGGTACTTGCCTGGGAATAGCTTTTCCCTCCCTCCCTCCCTCCCTCCC

tumor protein chr14:55922326-55922397

intron 8 (4 kb) 300 b 3' to exon 8

TCATAGCTCCTGTGAGTACCTGACTGTACACTGGTACCATTTT

retinoic acid induced 17 (RAI17)

chr14:20590072-20590114


CACCCCAAGNTCAGCACATGCCTCCCTCACCCTTGACTCTG

PIN2/TRF1-interacting protein (Pinx1) (SGP prediction)

chr14:54938405-54938445



CCATCTCATCAAGGCCTGCCTGGGATCTGCTACGGAGGATCTGAGTTGGGAGGGGTGCATTGT AK055056 brain protein

chr14:55698873-55698925 ?

CCCGAGGCACTGAGCACCCACAGCACCTCCCTGCCCGGTTGTTGCCCCTCCCTCATGGCATGTCTCACCACGATCCTGTTGCTACAT

Nociceptin precursor (Orphanin FQ) (PPNOC) (N23K/N27K)

chr14:56508153-56508239

3' UTR at the beginning of exon 3

CCTCCCTCATCCTCCCTCATCCTCCTCATCTACAGCAGATCCCCATCCTCCTCTCCTGCGGCAGTGTCCTCCCCG

no good gene prediciton chr14:58110355-58110429

3' UTR in minus?

TCCCTCATCCTCCCTCATCCTCCCCATCCTCCCTCATCCTCCCCATCCTCCCTCATCCTCCCTCATCCTCCCTCATCCTCCCCATCCTCCCTCATCCTCCCTCATCCTCCCTCATCCTCCCCATCCTCCCTCATCCtCCCCATCCTCCCTCA


GAGGGGTGCTTGGACTAGAGCCAGAAAGGGAGAGCAGACTCCGAGGGAACATGGGGAACTAAAGGACAC

heparan sulfate 6-sulfotransferase 3

chr14:110389946-110390014


AAACCCTATAAGCCCCTGCCCTCTTCCATCTCTTCTGTCTCTTTCT

myosin X (myo 10 gene) chr15:25745138-25745183


CACCTCTCATCCCGCTGCTCTCCCTCACATCATCAAACTGTAAGTCCACCTCTCATCCCGCTGCTCTCCCTCACATCATC

5'-AMP-activated protein kinase alpha-1

chr15:4980568-4980647


GATTTTATTCCTCTCTCCCAGTCCACCCTCCAACTGTTCCACATCCCATACCTCCTCCCTACGCCATGTTTTCATGAGGATGTCCTTCCCCTCCACCCACTCCAC

K+ voltage-gated channel Q 3

chr15:66444691-66444795

3' UTR

CCTGACGGATCCTGTGACGCCCACAGTATCCCTGTAGCAGACTGGCATGGCCTTGCCTGTGA

K+ voltage-gated channel Q 3

chr15:66654651-66654712


GAGACCTACCGGTTAGGCGTGCAAATGCATCCCGGCCAAGAAATCCATAACTCACCCTGACTGGTCGCA

D-factor/LIF receptor/MDR/MSDR2

chr15:6999514-6999583

exon 8

TCCCATGCATTCCATCATCTCCATCTTCTGCCATGACTTGCTTTTAATTTTATCCTTTTTTTGTCTCAACTTGAC

RNA-binding protein fxh chr15:77596576-77596651

intron 8 (4 kb) 1.5 kb 3' to exon 8 (exon 9 alternatively spliced)

CTACCCATCTCATCATCTATCCACCTATCCCATTCATCTATTCATCT

guanine nucleotide exchange factor cytohesin-4p

chr15:79341644-79341690

intron 9 700 b 3' to exon 9 (possible alternatively spliced 3 bp long exon 10)

AACATCCATCCCCACTTCCATTCTTCATTCTTTCCAAGTCTGTGACTGGTGAGTTATCTCCATCTTTGAAAATAGCTTTA

FLJ23082 (neural retina cDNA)

chr15:8076457-8076536

alternative exon 2 200 bp 3' from cryptic exonal splice site

GAGCGATGCTTCACCTTCTGATGGCTGGACGCTGGCCAAGCCTGTGCCTGCTGCTCACGCACTCACCA

NADH-cytochrome b5 reductase (b5R)

chr15:83947075-83947142 3' UTR

GACAGTAACCCGTCACCCCCGTGACAGTTAGCTGGTTGTGGGCCAGCATGGTGGGAGGAAGTGTCCCTGTGCAGTGGC no gene prediction

chr15:85779704-85779781

CAGCCTCATCCATCTCTTGCCCACCAGCCCACCCACCCCTCCATCTCTCG

similar to KIAA0767 protein chr15:86903217-86903262

intron 6 (17 kb) 3kb 3' to exon 6

GGTCTCATTCCTCTTCCCTTGGCATCAAGTCTCTACAGGATTAGGCGCATCTTCTCCCGCTGAGGTCAGAC no gene prediction

chr15:93662612-93662682 part of Lx4, L1 LINE repeat

CCACCTGCTCTGCTCAGACAGCCAGGCACCAGAAGTGAGAGCAGAAGTCTGCATCCTGCCGAGCTGCCG

probable Bax inhibitor-1 chr15:100324227-100324330

3' UTR only longer poly-adenylation site includes this 3' UTR; shorter expressed in testis

TGTAGCATGACTGTGGCATGATTGTAACATGTCTTCACCCCAGCTGCATGTGCTCACTTTGCATCTTCACTGCA

activin type IB receptor chr15:102163765-102163838


GACAGACCATAAATCCATGTGGGGACTGTGCCCCATTTGCATCTCATTTGGTCCCATCTGCCCCGGTTTCACGCG

BG807701 brain EST (BC036194 unknown protein)

chr16:28656086-28656160 intron (100 kb) 40 kb 3' to exon

AACCCCAGCCATTCTCATCAGCCTTACCATCAACCAGGTCTCCTGGGTCTACCTCTGAGACAACCACATCCTCACCATCA

KIAA1237 protein chr16:33521863-33521942

(5' UTR?) cloned from brain

ACCAAGTGGAAATCAGGAGAGGCAGAGGCATTATCTCGACATCTCCGTGGGTTCACTTTTCAATTTGTCCATCATTGCCATCATCATTGTT

Ataxin 2-binding protein, homologue of hexaribonucleotide binding protein 1

chr16:6366304-6366394


TCCTCACTGTGTGTCAATCAGGCACTGGAAGAATCTGCCACGGCTTTTCTCTCTGCCTGCCCTGCTCCCTCTCAC

ataxin 2-binding protein chr16:6435218-6435292

intron 4 (400 kb) 80 kb 5' of alternative promoter

CAAAGCTCTGCAGAGATGCCTTCATCCCCTCCATCCATCACAGCACAATTGCACTGGTGTGGACTCC

ataxin 2-binding protein chr16:6658766-6658832

exon 4 (35 kb) 2 kb 5' to exon 5 (3' to alternative promoters)

GCAAGACATGGCTGCCATCACATCCCTCACCACTGTCATGATAATCATCCATTCTTATCCCTGCTTGGACACCA

G-protein coupled inwardly rectifying K+ channel (Girk2A-2)

chr16:95855648-95855721

intron 2 (105 kb) 40 kb 5' to alternative promoter (same as 290a)

AGTGTCTGCATTTGGTGGCTGATTACGGGATGGATCCCTGGGTGTGGTTGTCTCTGCATGGTCCATCCTTATCAGTT

G-protein coupled inwardly rectifying K+ channel (Girk2A-1)

chr16:95889242-95889318

intron 2 (105 kb) 10 kb 3' to exon 2, 65 kb 5' of alternative promoter for Kir3.2d

ATTTCATTCCCCTCCCAGTNGGCCCTCCAACTGTTCCACATTCCATACCTCCTCCCCACTGGACTGTCTCCACAAGGATGTCCCCCACCTCCCACTCCAC

frabin alpha, beta chr16:15920017-15920116

intron 5 2.5 kb downstream of exon 5

CATTGTCTCTCCCCATCCATTTCTAACTCCATGAAATCAAACGTGTCTGAAGGTTCTCTTTGATTTGTTTGTTTTGTTGACCTTAAGG


ATCAGCAGTTCCGTTTACAGCTCACTCCATGTTCACACTTTCTGGCTGTGTGTTG

ribosomal protein S6 kinase, 90kD, polypeptide 2, mouse (RSK3)

chr17:7030714-7030768

3'UTR (aligns also to another genomic locus)

CCACCCTGAGCCCTGGCTACTCTCTCTCCTTCCCCCTCCCTCCTCTCTCCATGTGTTCCCTGCTAGCCTTTTCCTGTCT

pp90 ribosomal protein S6 kinase 3 (pp90RSK3)

chr17:7106440-7106518


TTGTAATGCCAGCATTCCTCTTCCCCATTTCCAGCTGTCACTCCTTCATTAAACTGCTGAGTCATTCAAA

afadin - AF-6 (trithorax (Drosophila) homolog)

chr17:12927724-12927790

3' UTR to last 10 b of 3' UTR of longest mRNA

TTCCAGGAGGAGCTCAGGTCACCCCCACCACCGCCGCCACTGCGTCTGCCGCCCTAGGCTTTCAGACATCATTAGTTCC

pacsin chr17:26910448-26910526

3' UTR

TTTTATCTCCGCTGTGCTTGTGTTGTCTGTAGCCCTGGGCGTCCTGGGCTGACCTTGGGGTCCCTTCC



GTGTGGCCTGTTTCCCACTCCGCATCCTACTCTTTCCTTCAGCACTCCTCACTCTCAAATCCTGCTCCAT

F-box protein FBX13 chr17:62226653-62226722


ACAACACTCTAGTGCTCTTTCTTTACTAGAGTTCGTTCATCATCCCCTGTGCTTCCCG

alpha-mannosidase II chr17:63746989-63747046


CAAACTCCTCTTCTACCCTACCTCTGTCAACTCCATGCCAACCACAGATCTGCTTGTAGCTCCTCAACACCGTG

3' to EF 1-gamma within gap chr17:85208596-85211891

CTATGACACCACCTTCACCTTCATCCTCTCATTGGAGGTTGCTGTTAGACTCTTGCTAGTCCAGGGACACATG

cyclin-box carrying protein chr18:9172990-9173062

3' UTR?

ATGCATCATCTATTTGTCTGTCTTCATGTCCATACATTTACTAATCATCTGTCTGTTTGTCCATCCATTCATCCATCTATCTCCATCCATCCATCCATATGGCTA

similar to early B-cell factor associated zinc finger protein

chr18:13950520-13950617


GCAGTGTGTCCACATACGCACAAGTGAGACACACACACCCTCTTCCTCCATCCTTCATGATCCACGGCTGCA

Bruno-like 4 (Brul4), RNA binding protein

chr18:25612484-25612555



CATCATTGACCGTGGCGTCCTGGTACTGCTGGTACTCGGACACCAGGTCATTCATGTTACTCTCGGCCTC

beta-5 tubulin chr18:67741552-67741621

3' UTR in minus

AAATCCATCACATTACGAAGCATTCAAATCATTTGTAAACACTCTTGGTTTCACTAG

basic transcription factor MITF-2B

chr18:69883232-69883289

intron 3 (45 kb)

TCTGTCCATGCATCCATCCATCCATCTATCCATCCGTACATCTGTCTATCTGTCCATCTGTCCATCCATCCACTG no gene prediction

chr18:77945443-77945517 part of (TGGA)n simple repeat

GTGCTCACACTGTACTCACGCTCACGCTCTGTGCTCACGCTCATGCTCTGTGCTCACATTGTACTCACGCTCACGCTCATGCTCTGTGCTCACGCTCTGCTCTGTGCTCACGCTCTGTGCTCACACTTACTTATTTGGTCAGTTAGTGCACTCACC

SET-binding protein (SEB) chr18:79533137-79533292


CACGCTCTGTGCTCACACTCTGTACTCACGCTCTGCTCTGTGCTCACACTGTACTCACGCTCACGCTCT SET-binding protein (SEB)

chr18:79533263-79533331


TTTCAGACCGTCCCTCACCTTCCCTGCTCAGCCCCATTGCTGTTCCTCCATCACTGTCTACAAC

neurexin II alpha & beta chr19:4322569-4322632

intron 17 (11 kb) or intron 1 (6 kb)

1400 downstream from exon 1 of n. beta

AGCTCCCATCATGCCAGCCCCACCCTCACCTCCATCTCTCCATTCCTCCTGCTCACCCT

neurexin II-alpha-b chr19:4323747-4323805

3' to alternative promoter

CCACGAGTGGGGTCAGGCATGTGGGTTTAAAGAGTTTTCCTTTGCAGAGCCTCATTTCATCCTTCATGGAGCTGCTCA no mRNA

chr19:5025277-5025354

TGGGGTCAGGCATGTGGGTTTAAAGAGTTTTCCTTTGCAGAGCCTCATTTCATCCTTCATGGAGCTGCTCAGGACTT

no good gene prediciton chr19:5025284-5025360

AGTGATTTCTCTGCCACATCGCCACCATGGGCCTTTGGCCTAATCA

no good gene predicted chr19:5026709-5026754

AACCAACCACCTGTTCTTCTTTCTCCTCCTGTCCCACATCATCGTCATGGAAAGCCTTGCCTGGTTCATCCTCTCGTACTTCGGCACTGGCTGGA

delta-6 desaturase chr19:9426985-9427079

exon 3

CTGACCTCTGGTCTTCACATGTGTGGGCAAGTACAGCTGCACACATGCGTACCCCTCTCTCCCTCATCCCCA

delta-5 desaturase chr19:9527077-9527142

intron 5 2 kb 3' from exon 6

TAAACCCCCACTATGGGGTCTCAACCCACAGCTCGAGAAACACTGTTGTAGATGCGTGCACTACTACT

GTP-binding protein alpha q subunit

chr19:15892861-15892928


CCTCCCATACCTCAAACTCACATCCACATGAAGCCTCACTATAGCGTTGAGGGGTTCGTGACTGGTGATG


GTTAACTTCATCCTTCCTTACTCCTCCCATGCTTCACACTACATACACATACAACA

VPS10 domain receptor chr19:48737630-48737685

3' UTR only in longer isoform

CACTCATTGTGTTTTTCCCAGTGAACTTCAATCTGCTGGTATTCATTTTCTATTTTTTTTACATTAA

CTCL tumor antigen L14-2 (myosin heavy chain homologue)

chr19:56846065-56846131

intron 2 500 b 3' of exon 2 (part of AT_rich, Low_complexity repeat)

GGATCGTCCAGCCCTTTCTCTGTGTGGCTTAAACCTAGGTTGCCATTGCTTTATACATTTTCACTTAGCA

AK025562 chrX:3324707-3324776

3' UTR

CGCTTCTGCATTGCAAATAAACAGTAGGCTTGGACCACTGCCGAGCATAGGGCTGGGAAGTCTTGGCTCA

glypican-3 (Gpc3) chrX:38162869-38162938


GTGGGTGAAACAGGCCTCCTGGCCATGTACGCCTGCCATGTCACTATAAAGCCAAATCAACAGGGTCAGGAC many ESTs

chrX:87923897-87923968 intron (20 kb)

1.5 kb 3' of exon (next exon is alternatively spliced)

ACATTTCCATATCATGCCTCACTACCACTGTGCTCCATGCTTCTGCGACAATGGCCCATTAAAGCCCCACTTAAAGTGTTCAG

hippocampal cDNA (Per1 interacting protein PIPS?)

chrX:115155741-115155822


GGCGCAGAGGGGGAAGAGCAGGACTCTGTGGCTCAGCGTGATCTTCCTGAACCCGAGTTTCCATTTCAGTATGATC

KIAA0443 (brain protein) chrX:115211837-115211912

GATCCATTCTGTCACCACCCTGCCCCTCACCATCCAGGTTCCATACTATCCAAAAGTTTGGGCT

midline 2 protein (mid 2/Fxy2)

chrX:120063482-120063545


AGGACTTGGTGGTGGGAGCTAGTTTTCAAATGTACTGAGGTGAGACAGCCCCAGTGCCCCCAACTTCATATG

FLJ30437 (brain protein) chrX:128321808-128321879

intron 2 ? (200 b) 50 b 5' to exon 3

ACAGCAACAAGCAGCAACGGTTAGCATGATGCCTGTGGCCCCTCATTCATCTCTCTACCCTCCTTC

upstream regulatory element binding protein 1 (UREB1) (tyrosine phosphorylated nuclear protein)

chrX:128930351-128930416

alternative part of exon 18 (of the longer isoform)

GACTGCAAGCTTCTGCCCATAAGGCCTGTGCTGACGCTGCCATTTCAAGCCCCTGCACAACCCATCTGT

RIKEN cDNA 1110012O05 (leucine zipper)

chrUn:63072951-63073019

3' UTR

GTCCACGTGCAATTTGCACACACACTTGGCTCGCATTCATCCCCTTTCCCACCGCCCCCTCACTCACCT

KIAA1423 chrUn:94487868-94487936

intron (3) 50 b 3' to exon (3)

CTTCATCTCCTGCCTCATTTCATGCCCCTGCCTCACACATTC

ring finger protein Fxy chrUn:118210332-118210374

intron 3 kb 5' to exon (10)

CACATATTCATCATCATATCCATCTTCATCTGGAACTCCAGTATTAGGGTCACAATCCCGGACTGTGAAC

coatomer protein gamma 2-subunit (COPG2)

chrUn:127872042-127872111

exon (1)

GGTGTTGGTTGATATAGACAGCAGGACGGTGGCCATGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTCAC

28S r RNA chrUn:114959958-114960030

GTGGAACCTGGCGCTAAACCATTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCT

28S rRNA chr16:10628954-10629029

4594

Ule CLIP Supporting Online Material Science2003

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