General information for g11480.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TSS | g11480.t2 | 16447649 | 16447649 |
| chr_1 | g11480 | g11480.t2 | isoform | g11480.t2 | 16447761 | 16448634 |
| chr_1 | g11480 | g11480.t2 | exon | g11480.t2.exon1 | 16447761 | 16447843 |
| chr_1 | g11480 | g11480.t2 | cds | g11480.t2.CDS1 | 16447761 | 16447843 |
| chr_1 | g11480 | g11480.t2 | exon | g11480.t2.exon2 | 16448189 | 16448324 |
| chr_1 | g11480 | g11480.t2 | cds | g11480.t2.CDS2 | 16448189 | 16448324 |
| chr_1 | g11480 | g11480.t2 | exon | g11480.t2.exon3 | 16448386 | 16448567 |
| chr_1 | g11480 | g11480.t2 | cds | g11480.t2.CDS3 | 16448386 | 16448567 |
| chr_1 | g11480 | g11480.t2 | exon | g11480.t2.exon4 | 16448633 | 16448634 |
| chr_1 | g11480 | g11480.t2 | cds | g11480.t2.CDS4 | 16448633 | 16448633 |
| chr_1 | g11480 | g11480.t2 | TTS | g11480.t2 | NA | NA |
Sequences
>g11480.t2 Gene=g11480 Length=403
ATGGCATCATCATCATCTGATGATTTATGGAGAAAGTGCGCTGACTGGCTTGTACGTTGC
AAAATTTTGCCAGCAGATCATAGGAGTAATTGGTTGACATCAGAAATTAAAACACTTGCA
TTGACACTTAGAGATGGAGTACTGCTTTGTAATCTGGTTCATTTTCTCGATCCTACAATG
GAAGCAATCGAATTTAATCGGAAGCCAAGAGATGCTCAGTTTTTGTGTCTGCAAAATATA
CGGATATTTTTGGAATGTTGCCGTAATAATTTTCAACTAAAGGAAAATGAATTGTTTGAA
TGTGGAATGCTGTATGATCTTACAAATTTTCATCGAGTATTAATTACACTATCCATACTT
TCTCAAAGTCGAAAAGTACAAAAAAATCATCCAAACTTGGCTG
>g11480.t2 Gene=g11480 Length=134
MASSSSDDLWRKCADWLVRCKILPADHRSNWLTSEIKTLALTLRDGVLLCNLVHFLDPTM
EAIEFNRKPRDAQFLCLQNIRIFLECCRNNFQLKENELFECGMLYDLTNFHRVLITLSIL
SQSRKVQKNHPNLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11480.t2 | Gene3D | G3DSA:1.10.418.10 | - | 5 | 133 | 0.000000 |
| 2 | g11480.t2 | PANTHER | PTHR45818 | PROTEIN VAV | 4 | 128 | 0.000000 |
| 1 | g11480.t2 | Pfam | PF00307 | Calponin homology (CH) domain | 11 | 122 | 0.000000 |
| 6 | g11480.t2 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 7 | 125 | 14.160000 |
| 4 | g11480.t2 | SMART | SM00033 | ch_5 | 9 | 120 | 0.000019 |
| 3 | g11480.t2 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 6 | 129 | 0.000000 |
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.
