General information for g11480.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein vav.
Parent gene
- The parent gene g11480 is located on chr_1: 16450950..16452667 (+ strand)
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.t3 | isoform | g11480.t3 | 16449700 | 16450885 |
| chr_1 | g11480 | g11480.t3 | exon | g11480.t3.exon1 | 16449700 | 16450885 |
| chr_1 | g11480 | g11480.t3 | cds | g11480.t3.CDS1 | 16449817 | 16450884 |
| chr_1 | g11480 | g11480.t3 | TSS | g11480.t3 | NA | NA |
| chr_1 | g11480 | g11480.t3 | TTS | g11480.t3 | NA | NA |
Sequences
>g11480.t3 Gene=g11480 Length=1186
AGACTATCGACAGCAGCAACATCAACTAGTTTGGGTCAACGTGACTATGTGATAAGAGAG
TTGGTCGAAACAGAATCTAACTATTGGATTGTACTAAATGATCTGAAATACAAATTTATG
CAACCTATGGAGAAGTTGCTAAAAGATGAGATTAAAATAATTTTCCCTCGAATAAAAGAA
TTGGTGGACATTCATAAAAAATTTCTAGACAAATTACGTGAAGCAACAGAGCCACATTCA
AAGTTTAAACTTAGTACAGTTTTTCTCGACTTTCGCGAACAATTTTTAATTTATGGAGAT
TATTGTTCTAAAATGACAGAAGCCACCGATACATTGAGAGATGTATGTAAGCGAAGTGCA
GCCATAGAGCAGCTTGTTATTCAGTGCCAGAAAGAACATAGTGGTGGAAGAGTGCAATTA
CGAGATATATTATCGGTACCTATGCAACGAATTTTAAAATATCATTTGTTATTAGATAAA
CTCGTACACGACACTCCAGCATCGCATGAAGATTTTAAAGGATTGCAGCGAGCAAAAGAA
GCGATGGTTGATGTTGCCCAATATATTAATGAAGTGAAACGTGATTGCGAACAGTTGAAT
GTTATAAAGAAAGTGCGCGAAAGTATAATTGATTTAAGTCTGCCTAATGGTAATGAATTA
TCGCAATATGGACGACTTCTTCTTGATGGAGATCTCAATATCAAAGCTCATGAAGATCAA
AAGCACAAACATCGTTACGGTTTTATTTTTGAGAAAATAATGATTCTTGTCAAAAATACA
AACACTCGAATTGGAGAGGGTGGTCAATATACATTTCGAGAAGCGTTTAATCTTGCAGAT
TACAAATTAATTGAAATGGGACATTCTAGAAAAACTTTAGGTAGAGATGCTAGGTTCAAA
TATCAGCTTTTATTAGCTAGAAAATCAAATGAAACGGCCTTTACAATTTATATGAAAACA
GAAATAGAAAGAGAAAAATGGATGAAAGCTTTGAATGATGCCATGGAAATTATTGAACCA
TTTGGCTGCAAAAATACTGACCATAAAATGGTTCTCACAACTTTTGAGAAGCCTACAATA
TGTCGTCATTGTTCACGTTTTCTTAAGGGTCTAATTCATCAAGGATATAAGTGTAAAGTG
TGCGAAATAAGTGTTCATAAGGGTTGCATTTCTTCAAGTGGAAGAT
>g11480.t3 Gene=g11480 Length=356
MQPMEKLLKDEIKIIFPRIKELVDIHKKFLDKLREATEPHSKFKLSTVFLDFREQFLIYG
DYCSKMTEATDTLRDVCKRSAAIEQLVIQCQKEHSGGRVQLRDILSVPMQRILKYHLLLD
KLVHDTPASHEDFKGLQRAKEAMVDVAQYINEVKRDCEQLNVIKKVRESIIDLSLPNGNE
LSQYGRLLLDGDLNIKAHEDQKHKHRYGFIFEKIMILVKNTNTRIGEGGQYTFREAFNLA
DYKLIEMGHSRKTLGRDARFKYQLLLARKSNETAFTIYMKTEIEREKWMKALNDAMEIIE
PFGCKNTDHKMVLTTFEKPTICRHCSRFLKGLIHQGYKCKVCEISVHKGCISSSGR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g11480.t3 | CDD | cd00160 | RhoGEF | 1 | 151 | 0.0000000 |
| 19 | g11480.t3 | CDD | cd01223 | PH_Vav | 169 | 301 | 0.0000000 |
| 17 | g11480.t3 | CDD | cd00029 | C1 | 309 | 352 | 0.0000000 |
| 13 | g11480.t3 | Gene3D | G3DSA:1.20.900.10 | - | 1 | 161 | 0.0000000 |
| 11 | g11480.t3 | Gene3D | G3DSA:2.30.29.30 | - | 164 | 302 | 0.0000000 |
| 12 | g11480.t3 | Gene3D | G3DSA:3.30.60.20 | - | 303 | 355 | 0.0000000 |
| 4 | g11480.t3 | PANTHER | PTHR45818:SF3 | PROTEIN VAV | 5 | 354 | 0.0000000 |
| 5 | g11480.t3 | PANTHER | PTHR45818 | PROTEIN VAV | 5 | 354 | 0.0000000 |
| 1 | g11480.t3 | Pfam | PF00621 | RhoGEF domain | 7 | 151 | 0.0000000 |
| 2 | g11480.t3 | Pfam | PF15411 | Pleckstrin homology domain | 183 | 292 | 0.0000011 |
| 3 | g11480.t3 | Pfam | PF00130 | Phorbol esters/diacylglycerol binding domain (C1 domain) | 309 | 352 | 0.0000000 |
| 14 | g11480.t3 | ProSiteProfiles | PS50010 | Dbl homology (DH) domain profile. | 1 | 153 | 25.5680000 |
| 16 | g11480.t3 | ProSiteProfiles | PS50003 | PH domain profile. | 186 | 297 | 11.5990000 |
| 15 | g11480.t3 | ProSiteProfiles | PS50081 | Zinc finger phorbol-ester/DAG-type profile. | 308 | 356 | 12.3940000 |
| 8 | g11480.t3 | SMART | SM00325 | RhoGEF_3 | 1 | 152 | 0.0000000 |
| 9 | g11480.t3 | SMART | SM00233 | PH_update | 187 | 299 | 0.0001300 |
| 10 | g11480.t3 | SMART | SM00109 | c1_12 | 309 | 356 | 0.0003300 |
| 7 | g11480.t3 | SUPERFAMILY | SSF48065 | DBL homology domain (DH-domain) | 5 | 169 | 0.0000000 |
| 6 | g11480.t3 | SUPERFAMILY | SSF50729 | PH domain-like | 178 | 334 | 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:0035556 | intracellular signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | 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.
