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.t1 TSS g11480.t1 16447649 16447649
chr_1 g11480 g11480.t1 isoform g11480.t1 16447761 16451820
chr_1 g11480 g11480.t1 exon g11480.t1.exon1 16447761 16447843
chr_1 g11480 g11480.t1 cds g11480.t1.CDS1 16447761 16447843
chr_1 g11480 g11480.t1 exon g11480.t1.exon2 16448189 16448324
chr_1 g11480 g11480.t1 cds g11480.t1.CDS2 16448189 16448324
chr_1 g11480 g11480.t1 exon g11480.t1.exon3 16448386 16448567
chr_1 g11480 g11480.t1 cds g11480.t1.CDS3 16448386 16448567
chr_1 g11480 g11480.t1 exon g11480.t1.exon4 16448633 16448722
chr_1 g11480 g11480.t1 cds g11480.t1.CDS4 16448633 16448722
chr_1 g11480 g11480.t1 exon g11480.t1.exon5 16449472 16449583
chr_1 g11480 g11480.t1 cds g11480.t1.CDS5 16449472 16449583
chr_1 g11480 g11480.t1 exon g11480.t1.exon6 16449700 16450885
chr_1 g11480 g11480.t1 cds g11480.t1.CDS6 16449700 16450885
chr_1 g11480 g11480.t1 exon g11480.t1.exon7 16450944 16451121
chr_1 g11480 g11480.t1 cds g11480.t1.CDS7 16450944 16451121
chr_1 g11480 g11480.t1 exon g11480.t1.exon8 16451181 16451443
chr_1 g11480 g11480.t1 cds g11480.t1.CDS8 16451181 16451443
chr_1 g11480 g11480.t1 exon g11480.t1.exon9 16451643 16451701
chr_1 g11480 g11480.t1 cds g11480.t1.CDS9 16451643 16451701
chr_1 g11480 g11480.t1 exon g11480.t1.exon10 16451764 16451820
chr_1 g11480 g11480.t1 cds g11480.t1.CDS10 16451764 16451820
chr_1 g11480 g11480.t1 TTS g11480.t1 16452592 16452592

Sequences

>g11480.t1 Gene=g11480 Length=2346
ATGGCATCATCATCATCTGATGATTTATGGAGAAAGTGCGCTGACTGGCTTGTACGTTGC
AAAATTTTGCCAGCAGATCATAGGAGTAATTGGTTGACATCAGAAATTAAAACACTTGCA
TTGACACTTAGAGATGGAGTACTGCTTTGTAATCTGGTTCATTTTCTCGATCCTACAATG
GAAGCAATCGAATTTAATCGGAAGCCAAGAGATGCTCAGTTTTTGTGTCTGCAAAATATA
CGGATATTTTTGGAATGTTGCCGTAATAATTTTCAACTAAAGGAAAATGAATTGTTTGAA
TGTGGAATGCTGTATGATCTTACAAATTTTCATCGAGTATTAATTACACTATCCATACTT
TCTCAAAGTCGAAAAGTACAAAAAAATCATCCAAACTTGGCTGGATTCAGCTATCAGTCT
GTTGCAAACGAGAGAAATTATAATGAAGAAGATATTTATAAAGAGCTACATTTGCATACA
AACACTTCTTCTATAACTCCATCGGAAAATGCAGCTTTTGATTGTAATGATGAAGAAAAC
ACTAAAGAAGAAGAGGTGTATCAAGATTTGTGTGCTATTCAAAATAATATTGTAAGAAAT
CAGAGACTATCGACAGCAGCAACATCAACTAGTTTGGGTCAACGTGACTATGTGATAAGA
GAGTTGGTCGAAACAGAATCTAACTATTGGATTGTACTAAATGATCTGAAATACAAATTT
ATGCAACCTATGGAGAAGTTGCTAAAAGATGAGATTAAAATAATTTTCCCTCGAATAAAA
GAATTGGTGGACATTCATAAAAAATTTCTAGACAAATTACGTGAAGCAACAGAGCCACAT
TCAAAGTTTAAACTTAGTACAGTTTTTCTCGACTTTCGCGAACAATTTTTAATTTATGGA
GATTATTGTTCTAAAATGACAGAAGCCACCGATACATTGAGAGATGTATGTAAGCGAAGT
GCAGCCATAGAGCAGCTTGTTATTCAGTGCCAGAAAGAACATAGTGGTGGAAGAGTGCAA
TTACGAGATATATTATCGGTACCTATGCAACGAATTTTAAAATATCATTTGTTATTAGAT
AAACTCGTACACGACACTCCAGCATCGCATGAAGATTTTAAAGGATTGCAGCGAGCAAAA
GAAGCGATGGTTGATGTTGCCCAATATATTAATGAAGTGAAACGTGATTGCGAACAGTTG
AATGTTATAAAGAAAGTGCGCGAAAGTATAATTGATTTAAGTCTGCCTAATGGTAATGAA
TTATCGCAATATGGACGACTTCTTCTTGATGGAGATCTCAATATCAAAGCTCATGAAGAT
CAAAAGCACAAACATCGTTACGGTTTTATTTTTGAGAAAATAATGATTCTTGTCAAAAAT
ACAAACACTCGAATTGGAGAGGGTGGTCAATATACATTTCGAGAAGCGTTTAATCTTGCA
GATTACAAATTAATTGAAATGGGACATTCTAGAAAAACTTTAGGTAGAGATGCTAGGTTC
AAATATCAGCTTTTATTAGCTAGAAAATCAAATGAAACGGCCTTTACAATTTATATGAAA
ACAGAAATAGAAAGAGAAAAATGGATGAAAGCTTTGAATGATGCCATGGAAATTATTGAA
CCATTTGGCTGCAAAAATACTGACCATAAAATGGTTCTCACAACTTTTGAGAAGCCTACA
ATATGTCGTCATTGTTCACGTTTTCTTAAGGGTCTAATTCATCAAGGATATAAGTGTAAA
GTGTGCGAAATAAGTGTTCATAAGGGTTGCATTTCTTCAAGTGGAAGATGTAAACAACCC
CCATTAGTGGTGGATAGATTTTTAGCTGAATTCAACTGGTTTGTTGGTACAATGGATAGA
GAAACTGCAACAACTAAATTGGAAAATCGTCGTGTAGGAACCTATTTACTCCGCCATCGT
CCTCAAGTTTCACATCCGACTGAAACTTTATTTGCATTAAGCCTTAAAACTGATAACAAA
GTTGTTAAGCATATGAAAATTTATCAAAAATCCGAAGATGGTCATCAACATTTCTTTTTG
TCTTCACGACGATATTTTCGAACTGTCGTTGAACTCGTATCTTTTTATGAGCGAAATGAT
TTGGGTGAAAATTTTGCTGGATTAAACCAAATGCTTTTGTGGCCATTTTATGAAAGAACA
GCAACAGCAATTTATGACTTTACACCAAGCGAACCTAATCAGCTTCCACTAAAAAAAGGC
TGCTTAATATACATAATCAGTAAAGAGGGAGATAGTAGAGGATGGCTTAAAGGGAGATCC
ATGGATAGAATTGGTTTCTTTCCAAAAGGATATGTGCAAGAGAACTGTCCAAATGATGAT
CTATGA

>g11480.t1 Gene=g11480 Length=781
MASSSSDDLWRKCADWLVRCKILPADHRSNWLTSEIKTLALTLRDGVLLCNLVHFLDPTM
EAIEFNRKPRDAQFLCLQNIRIFLECCRNNFQLKENELFECGMLYDLTNFHRVLITLSIL
SQSRKVQKNHPNLAGFSYQSVANERNYNEEDIYKELHLHTNTSSITPSENAAFDCNDEEN
TKEEEVYQDLCAIQNNIVRNQRLSTAATSTSLGQRDYVIRELVETESNYWIVLNDLKYKF
MQPMEKLLKDEIKIIFPRIKELVDIHKKFLDKLREATEPHSKFKLSTVFLDFREQFLIYG
DYCSKMTEATDTLRDVCKRSAAIEQLVIQCQKEHSGGRVQLRDILSVPMQRILKYHLLLD
KLVHDTPASHEDFKGLQRAKEAMVDVAQYINEVKRDCEQLNVIKKVRESIIDLSLPNGNE
LSQYGRLLLDGDLNIKAHEDQKHKHRYGFIFEKIMILVKNTNTRIGEGGQYTFREAFNLA
DYKLIEMGHSRKTLGRDARFKYQLLLARKSNETAFTIYMKTEIEREKWMKALNDAMEIIE
PFGCKNTDHKMVLTTFEKPTICRHCSRFLKGLIHQGYKCKVCEISVHKGCISSSGRCKQP
PLVVDRFLAEFNWFVGTMDRETATTKLENRRVGTYLLRHRPQVSHPTETLFALSLKTDNK
VVKHMKIYQKSEDGHQHFFLSSRRYFRTVVELVSFYERNDLGENFAGLNQMLLWPFYERT
ATAIYDFTPSEPNQLPLKKGCLIYIISKEGDSRGWLKGRSMDRIGFFPKGYVQENCPNDD
L

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g11480.t1 CDD cd00160 RhoGEF 215 391 2.02129E-37
23 g11480.t1 CDD cd01223 PH_Vav 409 541 2.29427E-48
20 g11480.t1 CDD cd00029 C1 549 592 7.70798E-11
22 g11480.t1 CDD cd00174 SH3 720 771 1.81511E-13
19 g11480.t1 Coils Coil Coil 778 781 -
13 g11480.t1 Gene3D G3DSA:1.10.418.10 - 5 177 4.5E-41
17 g11480.t1 Gene3D G3DSA:1.20.900.10 - 211 401 2.6E-52
15 g11480.t1 Gene3D G3DSA:2.30.29.30 - 404 542 2.8E-26
16 g11480.t1 Gene3D G3DSA:3.30.60.20 - 546 601 3.8E-15
18 g11480.t1 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 603 726 1.5E-22
14 g11480.t1 Gene3D G3DSA:2.30.30.40 SH3 Domains 727 775 8.2E-13
7 g11480.t1 PANTHER PTHR45818 PROTEIN VAV 4 598 4.5E-212
6 g11480.t1 PANTHER PTHR45818 PROTEIN VAV 609 773 4.5E-212
4 g11480.t1 Pfam PF00307 Calponin homology (CH) domain 12 122 2.1E-10
2 g11480.t1 Pfam PF00621 RhoGEF domain 218 391 1.5E-40
5 g11480.t1 Pfam PF00130 Phorbol esters/diacylglycerol binding domain (C1 domain) 549 592 1.6E-9
3 g11480.t1 Pfam PF00017 SH2 domain 613 696 1.0E-9
1 g11480.t1 Pfam PF00018 SH3 domain 722 769 1.4E-10
24 g11480.t1 ProSitePatterns PS00479 Zinc finger phorbol-ester/DAG-type signature. 549 597 -
33 g11480.t1 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 7 125 14.16
31 g11480.t1 ProSiteProfiles PS50010 Dbl homology (DH) domain profile. 214 393 31.583
36 g11480.t1 ProSiteProfiles PS50003 PH domain profile. 426 537 11.599
35 g11480.t1 ProSiteProfiles PS50081 Zinc finger phorbol-ester/DAG-type profile. 548 597 12.86
34 g11480.t1 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 613 716 16.129
32 g11480.t1 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 716 777 21.951
28 g11480.t1 SMART SM00033 ch_5 9 120 1.9E-5
26 g11480.t1 SMART SM00325 RhoGEF_3 218 392 5.7E-41
27 g11480.t1 SMART SM00233 PH_update 427 539 1.3E-4
30 g11480.t1 SMART SM00109 c1_12 549 597 2.0E-6
29 g11480.t1 SMART SM00252 SH2_5 611 702 3.5E-16
25 g11480.t1 SMART SM00326 SH3_2 719 776 3.5E-14
8 g11480.t1 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 6 136 9.43E-22
10 g11480.t1 SUPERFAMILY SSF48065 DBL homology domain (DH-domain) 210 408 2.09E-46
9 g11480.t1 SUPERFAMILY SSF50729 PH domain-like 418 574 7.99E-18
11 g11480.t1 SUPERFAMILY SSF55550 SH2 domain 608 718 3.77E-19
12 g11480.t1 SUPERFAMILY SSF50044 SH3-domain 711 774 6.83E-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
GO:0005085 guanyl-nucleotide exchange factor activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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