General information for g13030.t4
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.t4 | isoform | g13030.t4 | 27594573 | 27595760 |
| chr_1 | g13030 | g13030.t4 | exon | g13030.t4.exon1 | 27594573 | 27595564 |
| chr_1 | g13030 | g13030.t4 | cds | g13030.t4.CDS1 | 27594575 | 27595105 |
| chr_1 | g13030 | g13030.t4 | exon | g13030.t4.exon2 | 27595621 | 27595760 |
| chr_1 | g13030 | g13030.t4 | TSS | g13030.t4 | NA | NA |
| chr_1 | g13030 | g13030.t4 | TTS | g13030.t4 | NA | NA |
Sequences
>g13030.t4 Gene=g13030 Length=1132
GTCAACAAAGTAAAGGAACATCACCACAAGCTGAATCATTGGCTCGTGAAATGATTGACA
AATTGGATGAATTAGATCAAAATATTTTACAAGCTGTTATTAATGTTGATAAAGCTGGTC
TTCAACAAACTGCGCATACTGTTCAAGGACGTTTAGAACAAGCAATTCGTTGGTTAACAA
ATCCTGGGGCTGATGACAAAGGCTTGGGTCAACGTGCTATTGCACTTATCATTGAAGAAG
GAAAGAAAGTTGCCGATGGCTTGCCAGGACATCAAAAGTCCGATATTCTCTATCTTTGTG
ATGAAGTAGAAAATCTTGCCAATTAATATTCAAAATTGTGTTCAGCGGGCTTGGCTCACA
CACCCGAAGCTCAAGAAATTGCTCGCAAATTAAATGCAAAATTGCATGAGTTGAAGAATT
TGATTCAATCAGCCGTTGTTGGTCGTGTAGTTGAAGATTTTATCGATATTTCAACGCCAT
TGAAACAATTTACTGAAGCTGTCAATGCACCAGAAGGAACACCGAATCGCGAACAAAATT
TCAACCAAAAGGCGGCAAATTTGCAAGCATTCAGTGACCGTGCATCAAAGACAAGTCGAA
TGGTTGCTGCTGGTGGTTCAGGTGGAAACAAAAAACTCGCTGAAGTTCTTCTTGCATCAG
CTGCACAAATTGATAGTCTTACACCACAACTTATTAGTGCTGGTCGTATTCGTATGAATT
ATCCAGGATCAAAGGCTGCTGAAGAACATTATAATAATCTTAAGCAACAATATGCTGACA
CTATTTTGAGAATGAGAACTCTCTGCGATCAAGCAACTGATCCAGCTGATTTCATCAAAG
CCAGTGAAGAACAAATGCAAAAACACACATTATTGTGCGAAGATGCAATTAGAAATCGAG
TCCCACAAAAAATGGTTGACAACACAAGCAGCATTGCACGTTTGGCCAATCGTGTATTGT
TAGTTGCCAAACAAGAAGCTGACAATTCTGAAGATCCACAATTTACCTCAGAATTGCTTA
ATGCTTCCGATAAGCTTCAAAATTCAGTTCCGACAATGGTACAAAATGCTAAATCTGTTG
CAACTGACATTACGAATGGGGCTGCTGGTGCTAATTGGCGTGATGCGAATAA
>g13030.t4 Gene=g13030 Length=177
MVAAGGSGGNKKLAEVLLASAAQIDSLTPQLISAGRIRMNYPGSKAAEEHYNNLKQQYAD
TILRMRTLCDQATDPADFIKASEEQMQKHTLLCEDAIRNRVPQKMVDNTSSIARLANRVL
LVAKQEADNSEDPQFTSELLNASDKLQNSVPTMVQNAKSVATDITNGAAGANWRDAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13030.t4 | Coils | Coil | Coil | 79 | 99 | - |
| 6 | g13030.t4 | Gene3D | G3DSA:1.20.120.810 | - | 1 | 73 | 7.8E-19 |
| 7 | g13030.t4 | Gene3D | G3DSA:1.20.120.230 | - | 76 | 177 | 7.6E-41 |
| 2 | g13030.t4 | PANTHER | PTHR46180:SF1 | VINCULIN | 1 | 176 | 2.4E-56 |
| 3 | g13030.t4 | PANTHER | PTHR46180 | VINCULIN | 1 | 176 | 2.4E-56 |
| 1 | g13030.t4 | Pfam | PF01044 | Vinculin family | 2 | 176 | 1.0E-62 |
| 4 | g13030.t4 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 4 | 74 | 1.73E-18 |
| 5 | g13030.t4 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 76 | 177 | 9.42E-34 |
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 |
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.
