General information for g13030.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vinculin.
Parent gene
- The parent gene g13030 is located on chr_1: 27595760..27604584 (- 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 | g13030 | g13030.t5 | isoform | g13030.t5 | 27595760 | 27604584 |
| chr_1 | g13030 | g13030.t5 | exon | g13030.t5.exon1 | 27595760 | 27596715 |
| chr_1 | g13030 | g13030.t5 | cds | g13030.t5.CDS1 | 27595762 | 27596715 |
| chr_1 | g13030 | g13030.t5 | exon | g13030.t5.exon2 | 27604528 | 27604584 |
| chr_1 | g13030 | g13030.t5 | cds | g13030.t5.CDS2 | 27604528 | 27604584 |
| chr_1 | g13030 | g13030.t5 | TSS | g13030.t5 | 27604809 | 27604809 |
| chr_1 | g13030 | g13030.t5 | TTS | g13030.t5 | NA | NA |
Sequences
>g13030.t5 Gene=g13030 Length=1013
ATGCCAGTTTTTCACACAAAGACGATTGAATCAATTTTGGAACCAGTCGCAAATCAGGTT
TCACGACTGGTGATTCTTCACGAAGAAGCAGAAGATGGAAATGCTATGCCAGATTTGTCA
AGACCCGTCCATGGAGTCTCAATTGCTGTCACAAATCTTGTTAAAGTTGGCAGAGAAACA
ATCAATAGTTCTGATGATCAAATTCTTAAACAAGACATGCCTTCTGCATTAATGCGTGTT
GAAACTGCATCACAATTATTAGAAGAAGCTTCTTCACTTCTTCGTGCTGATCCATATTCA
GGACCTGCTCGTCGTAAGCTTATTGAAGGATCACGTGGCATTCTTCAAGGCACATCACAA
CTTTTATTATGTTTTGATGAATCAGAAGTACGAAAAATTGTTCGCGAATGTAAACGTGTC
CTTGACTATCTCGCTGTAAGTGAGGTCATTGACACAATGGAAGATTTGGTACAATTTCTT
AAAGATCTCAGTCCATGTCTAAGTAAAGTATCACGTGAAGTCAGCAATCGTGAAAAAGAA
TTGACTCATCAAGTTCATAGTGAAATTCTTGTCAGATGCCTCGAACAAGTGAAAATTCTC
GCGCCAATTCTTATTTGCAGCATGAAAGTTTACATTCATATCATGGAGCAAGGTGGAAAA
GGTTCAGAAGAAGCTGCCGAAAATCGTAATTATCTTGCAGCAAGAATGACAGATGAAATT
CAAGAAATTATTCGTGTATTGCAATTGACAACATATGATGAAGACACAAGTGAACTTGAC
AATCTTACAGTGCTTAAAAAGATCAACAATGCCATTCGCAATAAAATGGAAGCTGCCAAA
GATTGGCTTAAGAATCCATACGCACTTAAGGGTGGCATTGGTGAAAAAGCTCTTCGACAG
ATTATCGATAATGCCCATAAAGTTGCCGACCGTTGCTTGCCAAGCGATTCTTACCGAATT
CGTCGTAATGCTGATGATTTGACTGCCATGGCAAATGCCTTATGCGAATTACG
>g13030.t5 Gene=g13030 Length=337
MPVFHTKTIESILEPVANQVSRLVILHEEAEDGNAMPDLSRPVHGVSIAVTNLVKVGRET
INSSDDQILKQDMPSALMRVETASQLLEEASSLLRADPYSGPARRKLIEGSRGILQGTSQ
LLLCFDESEVRKIVRECKRVLDYLAVSEVIDTMEDLVQFLKDLSPCLSKVSREVSNREKE
LTHQVHSEILVRCLEQVKILAPILICSMKVYIHIMEQGGKGSEEAAENRNYLAARMTDEI
QEIIRVLQLTTYDEDTSELDNLTVLKKINNAIRNKMEAAKDWLKNPYALKGGIGEKALRQ
IIDNAHKVADRCLPSDSYRIRRNADDLTAMANALCEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13030.t5 | Gene3D | G3DSA:1.20.120.230 | - | 1 | 128 | 5.6E-55 |
| 9 | g13030.t5 | Gene3D | G3DSA:1.20.120.230 | - | 129 | 254 | 2.8E-56 |
| 7 | g13030.t5 | Gene3D | G3DSA:1.20.120.810 | - | 255 | 337 | 1.1E-31 |
| 2 | g13030.t5 | PANTHER | PTHR46180:SF1 | VINCULIN | 4 | 337 | 1.2E-149 |
| 3 | g13030.t5 | PANTHER | PTHR46180 | VINCULIN | 4 | 337 | 1.2E-149 |
| 1 | g13030.t5 | Pfam | PF01044 | Vinculin family | 3 | 337 | 6.6E-144 |
| 6 | g13030.t5 | ProSitePatterns | PS00664 | Vinculin repeated domain signature. | 276 | 286 | - |
| 5 | g13030.t5 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 38 | 248 | 2.07E-56 |
| 4 | g13030.t5 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 252 | 337 | 3.87E-25 |
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:0051015 | actin filament binding | MF |
| GO:0003779 | actin binding | MF |
| GO:0007155 | cell adhesion | BP |
| GO:0015629 | actin cytoskeleton | CC |
| GO:0005198 | structural molecule 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.
