Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t5 isoform g11480.t5 16450950 16452667
chr_1 g11480 g11480.t5 exon g11480.t5.exon1 16450950 16451121
chr_1 g11480 g11480.t5 cds g11480.t5.CDS1 16451006 16451121
chr_1 g11480 g11480.t5 exon g11480.t5.exon2 16451181 16451443
chr_1 g11480 g11480.t5 cds g11480.t5.CDS2 16451181 16451443
chr_1 g11480 g11480.t5 exon g11480.t5.exon3 16451643 16451701
chr_1 g11480 g11480.t5 cds g11480.t5.CDS3 16451643 16451701
chr_1 g11480 g11480.t5 exon g11480.t5.exon4 16451764 16452667
chr_1 g11480 g11480.t5 cds g11480.t5.CDS4 16451764 16451820
chr_1 g11480 g11480.t5 TSS g11480.t5 NA NA
chr_1 g11480 g11480.t5 TTS g11480.t5 NA NA

Sequences

>g11480.t5 Gene=g11480 Length=1398
AACCCCCATTAGTGGTGGATAGATTTTTAGCTGAATTCAACTGGTTTGTTGGTACAATGG
ATAGAGAAACTGCAACAACTAAATTGGAAAATCGTCGTGTAGGAACCTATTTACTCCGCC
ATCGTCCTCAAGTTTCACATCCGACTGAAACTTTATTTGCATTAAGCCTTAAAACTGATA
ACAAAGTTGTTAAGCATATGAAAATTTATCAAAAATCCGAAGATGGTCATCAACATTTCT
TTTTGTCTTCACGACGATATTTTCGAACTGTCGTTGAACTCGTATCTTTTTATGAGCGAA
ATGATTTGGGTGAAAATTTTGCTGGATTAAACCAAATGCTTTTGTGGCCATTTTATGAAA
GAACAGCAACAGCAATTTATGACTTTACACCAAGCGAACCTAATCAGCTTCCACTAAAAA
AAGGCTGCTTAATATACATAATCAGTAAAGAGGGAGATAGTAGAGGATGGCTTAAAGGGA
GATCCATGGATAGAATTGGTTTCTTTCCAAAAGGATATGTGCAAGAGAACTGTCCAAATG
ATGATCTATGATTTTATGATGAATATGTCAACTACTATTTCGTTTATATCGAACCTTCTG
CTTTAATTCAATAGATAATTTGACAGTGCTCAAATCTTATGAAATTAAAACTACAATTTA
GAAGAATACCAAAGGTAATACTTAATCCTCGAAATCTAAAAAAACTAAAAAAATTATAAT
AAACTTTTAATGTAGCCATTCCTATTTATGCGATCTTACTTTTATGTATTTCAACTTTAA
ACTGAAATTTTAAATGCAATTTAAATTCAATGTGACGATGTAAGAATTTCGAATATTTCT
CTTCACTTCTCTTCCTTAACTGTTACTTATAAGATGATGCATGTTTAAAATGATGTTAAT
GAAACGTATTTTATATGGTCAAGTTTTAAAATTTCATACAAGTTTTATTTATTCATATTT
GGACATAAAAAAATGTTCAAGCGAGGAATTAAAATAATATATAAAATTATTTTTTATAGA
TTCTTTTATTGTTTATTGCAAAATGCAATAAAAGTCTAATAAATAAAAAATTGCAGTCGT
AGATAAAGTCGTCCATTCATACCTCTTTAATGGTGTGAATAAGTATGAAAAATATATATA
AAGTCAGTTGAATTACATTGTATTGGTTTAAGGACAAAAATGAGAAAGAAATTATGAATA
TCATAACATGATAAAAATGAATAAGATCACAAAATAAAACACAAAATATTTATAAAATTC
GATGCCTTTCGAATAGAGGTAAAGAAAAATAAATATCCAGTAAAGTAAATGAAATTTAAA
AACAACTTTTTTGTCTCTCATTTGTTTTTCTCTAACTAGTAATAATTTACTAAAAGAATT
GCAGTTTAAATAGGTGTT

>g11480.t5 Gene=g11480 Length=164
MDRETATTKLENRRVGTYLLRHRPQVSHPTETLFALSLKTDNKVVKHMKIYQKSEDGHQH
FFLSSRRYFRTVVELVSFYERNDLGENFAGLNQMLLWPFYERTATAIYDFTPSEPNQLPL
KKGCLIYIISKEGDSRGWLKGRSMDRIGFFPKGYVQENCPNDDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11480.t5 CDD cd00174 SH3 103 154 0.0000000
10 g11480.t5 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 1 109 0.0000000
9 g11480.t5 Gene3D G3DSA:2.30.30.40 SH3 Domains 110 158 0.0000000
3 g11480.t5 PANTHER PTHR45818 PROTEIN VAV 1 156 0.0000000
6 g11480.t5 PRINTS PR00452 SH3 domain signature 102 112 0.0000270
4 g11480.t5 PRINTS PR00452 SH3 domain signature 116 131 0.0000270
5 g11480.t5 PRINTS PR00452 SH3 domain signature 146 158 0.0000270
2 g11480.t5 Pfam PF00017 SH2 domain 2 79 0.0000001
1 g11480.t5 Pfam PF00018 SH3 domain 105 152 0.0000000
15 g11480.t5 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 1 99 13.4590000
14 g11480.t5 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 99 160 21.9510000
13 g11480.t5 SMART SM00252 SH2_5 1 85 0.0000002
12 g11480.t5 SMART SM00326 SH3_2 102 159 0.0000000
7 g11480.t5 SUPERFAMILY SSF55550 SH2 domain 1 101 0.0000000
8 g11480.t5 SUPERFAMILY SSF50044 SH3-domain 94 157 0.0000000

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

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