Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein vav.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11480 g11480.t4 isoform g11480.t4 16450338 16452667
chr_1 g11480 g11480.t4 exon g11480.t4.exon1 16450338 16450885
chr_1 g11480 g11480.t4 cds g11480.t4.CDS1 16450459 16450885
chr_1 g11480 g11480.t4 exon g11480.t4.exon2 16450944 16451121
chr_1 g11480 g11480.t4 cds g11480.t4.CDS2 16450944 16451121
chr_1 g11480 g11480.t4 exon g11480.t4.exon3 16451181 16451443
chr_1 g11480 g11480.t4 cds g11480.t4.CDS3 16451181 16451443
chr_1 g11480 g11480.t4 exon g11480.t4.exon4 16451643 16451701
chr_1 g11480 g11480.t4 cds g11480.t4.CDS4 16451643 16451701
chr_1 g11480 g11480.t4 exon g11480.t4.exon5 16451764 16452667
chr_1 g11480 g11480.t4 cds g11480.t4.CDS5 16451764 16451820
chr_1 g11480 g11480.t4 TSS g11480.t4 NA NA
chr_1 g11480 g11480.t4 TTS g11480.t4 NA NA

Sequences

>g11480.t4 Gene=g11480 Length=1952
TCTGCCTAATGGTAATGAATTATCGCAATATGGACGACTTCTTCTTGATGGAGATCTCAA
TATCAAAGCTCATGAAGATCAAAAGCACAAACATCGTTACGGTTTTATTTTTGAGAAAAT
AATGATTCTTGTCAAAAATACAAACACTCGAATTGGAGAGGGTGGTCAATATACATTTCG
AGAAGCGTTTAATCTTGCAGATTACAAATTAATTGAAATGGGACATTCTAGAAAAACTTT
AGGTAGAGATGCTAGGTTCAAATATCAGCTTTTATTAGCTAGAAAATCAAATGAAACGGC
CTTTACAATTTATATGAAAACAGAAATAGAAAGAGAAAAATGGATGAAAGCTTTGAATGA
TGCCATGGAAATTATTGAACCATTTGGCTGCAAAAATACTGACCATAAAATGGTTCTCAC
AACTTTTGAGAAGCCTACAATATGTCGTCATTGTTCACGTTTTCTTAAGGGTCTAATTCA
TCAAGGATATAAGTGTAAAGTGTGCGAAATAAGTGTTCATAAGGGTTGCATTTCTTCAAG
TGGAAGATGTAAACAACCCCCATTAGTGGTGGATAGATTTTTAGCTGAATTCAACTGGTT
TGTTGGTACAATGGATAGAGAAACTGCAACAACTAAATTGGAAAATCGTCGTGTAGGAAC
CTATTTACTCCGCCATCGTCCTCAAGTTTCACATCCGACTGAAACTTTATTTGCATTAAG
CCTTAAAACTGATAACAAAGTTGTTAAGCATATGAAAATTTATCAAAAATCCGAAGATGG
TCATCAACATTTCTTTTTGTCTTCACGACGATATTTTCGAACTGTCGTTGAACTCGTATC
TTTTTATGAGCGAAATGATTTGGGTGAAAATTTTGCTGGATTAAACCAAATGCTTTTGTG
GCCATTTTATGAAAGAACAGCAACAGCAATTTATGACTTTACACCAAGCGAACCTAATCA
GCTTCCACTAAAAAAAGGCTGCTTAATATACATAATCAGTAAAGAGGGAGATAGTAGAGG
ATGGCTTAAAGGGAGATCCATGGATAGAATTGGTTTCTTTCCAAAAGGATATGTGCAAGA
GAACTGTCCAAATGATGATCTATGATTTTATGATGAATATGTCAACTACTATTTCGTTTA
TATCGAACCTTCTGCTTTAATTCAATAGATAATTTGACAGTGCTCAAATCTTATGAAATT
AAAACTACAATTTAGAAGAATACCAAAGGTAATACTTAATCCTCGAAATCTAAAAAAACT
AAAAAAATTATAATAAACTTTTAATGTAGCCATTCCTATTTATGCGATCTTACTTTTATG
TATTTCAACTTTAAACTGAAATTTTAAATGCAATTTAAATTCAATGTGACGATGTAAGAA
TTTCGAATATTTCTCTTCACTTCTCTTCCTTAACTGTTACTTATAAGATGATGCATGTTT
AAAATGATGTTAATGAAACGTATTTTATATGGTCAAGTTTTAAAATTTCATACAAGTTTT
ATTTATTCATATTTGGACATAAAAAAATGTTCAAGCGAGGAATTAAAATAATATATAAAA
TTATTTTTTATAGATTCTTTTATTGTTTATTGCAAAATGCAATAAAAGTCTAATAAATAA
AAAATTGCAGTCGTAGATAAAGTCGTCCATTCATACCTCTTTAATGGTGTGAATAAGTAT
GAAAAATATATATAAAGTCAGTTGAATTACATTGTATTGGTTTAAGGACAAAAATGAGAA
AGAAATTATGAATATCATAACATGATAAAAATGAATAAGATCACAAAATAAAACACAAAA
TATTTATAAAATTCGATGCCTTTCGAATAGAGGTAAAGAAAAATAAATATCCAGTAAAGT
AAATGAAATTTAAAAACAACTTTTTTGTCTCTCATTTGTTTTTCTCTAACTAGTAATAAT
TTACTAAAAGAATTGCAGTTTAAATAGGTGTT

>g11480.t4 Gene=g11480 Length=327
MILVKNTNTRIGEGGQYTFREAFNLADYKLIEMGHSRKTLGRDARFKYQLLLARKSNETA
FTIYMKTEIEREKWMKALNDAMEIIEPFGCKNTDHKMVLTTFEKPTICRHCSRFLKGLIH
QGYKCKVCEISVHKGCISSSGRCKQPPLVVDRFLAEFNWFVGTMDRETATTKLENRRVGT
YLLRHRPQVSHPTETLFALSLKTDNKVVKHMKIYQKSEDGHQHFFLSSRRYFRTVVELVS
FYERNDLGENFAGLNQMLLWPFYERTATAIYDFTPSEPNQLPLKKGCLIYIISKEGDSRG
WLKGRSMDRIGFFPKGYVQENCPNDDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11480.t4 CDD cd00029 C1 95 138 4.1429E-11
15 g11480.t4 CDD cd00174 SH3 266 317 7.4643E-14
11 g11480.t4 Gene3D G3DSA:2.30.29.30 - 1 88 1.2E-10
12 g11480.t4 Gene3D G3DSA:3.30.60.20 - 92 147 1.1E-15
13 g11480.t4 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 149 272 3.2E-23
10 g11480.t4 Gene3D G3DSA:2.30.30.40 SH3 Domains 273 321 2.5E-13
5 g11480.t4 PANTHER PTHR45818 PROTEIN VAV 2 144 8.0E-68
4 g11480.t4 PANTHER PTHR45818 PROTEIN VAV 155 319 8.0E-68
3 g11480.t4 Pfam PF00130 Phorbol esters/diacylglycerol binding domain (C1 domain) 95 138 5.0E-10
2 g11480.t4 Pfam PF00017 SH2 domain 159 242 2.6E-10
1 g11480.t4 Pfam PF00018 SH3 domain 268 315 4.5E-11
16 g11480.t4 ProSitePatterns PS00479 Zinc finger phorbol-ester/DAG-type signature. 95 143 -
23 g11480.t4 ProSiteProfiles PS50003 PH domain profile. 1 83 9.443
22 g11480.t4 ProSiteProfiles PS50081 Zinc finger phorbol-ester/DAG-type profile. 94 143 12.86
21 g11480.t4 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 159 262 16.129
20 g11480.t4 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 262 323 21.951
19 g11480.t4 SMART SM00109 c1_12 95 143 2.0E-6
18 g11480.t4 SMART SM00252 SH2_5 157 248 3.5E-16
17 g11480.t4 SMART SM00326 SH3_2 265 322 3.5E-14
7 g11480.t4 SUPERFAMILY SSF50729 PH domain-like 13 120 1.2E-9
6 g11480.t4 SUPERFAMILY SSF57889 Cysteine-rich domain 92 139 2.24E-13
8 g11480.t4 SUPERFAMILY SSF55550 SH2 domain 154 264 8.21E-20
9 g11480.t4 SUPERFAMILY SSF50044 SH3-domain 257 320 1.97E-17

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF
GO:0035556 intracellular signal transduction BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values