General information for g13030.t3
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.t3 | isoform | g13030.t3 | 27591873 | 27594146 |
| chr_1 | g13030 | g13030.t3 | exon | g13030.t3.exon1 | 27591873 | 27592492 |
| chr_1 | g13030 | g13030.t3 | cds | g13030.t3.CDS1 | 27592429 | 27592492 |
| chr_1 | g13030 | g13030.t3 | exon | g13030.t3.exon2 | 27593369 | 27593463 |
| chr_1 | g13030 | g13030.t3 | cds | g13030.t3.CDS2 | 27593369 | 27593463 |
| chr_1 | g13030 | g13030.t3 | exon | g13030.t3.exon3 | 27593520 | 27594146 |
| chr_1 | g13030 | g13030.t3 | cds | g13030.t3.CDS3 | 27593520 | 27593945 |
| chr_1 | g13030 | g13030.t3 | TSS | g13030.t3 | NA | NA |
| chr_1 | g13030 | g13030.t3 | TTS | g13030.t3 | NA | NA |
Sequences
>g13030.t3 Gene=g13030 Length=1342
TTGCTTCAAAATGTCCGAAATGTTCGTAATGCAATCACACAACAACCAGAAATCCCAGCA
CCACCAGATCTTTCAGCACTTCGACTTAATGCAGAATCGCATGTTCCGCCACCAAGACCA
CCATTGCCACGTGAAGAAATTCCACCAGTTCGTCCTCCACCACCTGAAACTGATGATGAA
GATGAAGGCGTTTTCAAGGCAATGCCAACATCTAATCAACCAATTTTGCTTGCCGCTCAT
GGACTTCATCAAGAAGTTCGTCAATGGTCATCAAAGGACAATGAAATTATTGCAGCTGCT
AAACGTATGGCTGTTTTAATGGCTCGCTTGTCAGAACTTGTTCATCAAGACTCGAAAGGA
AGCAAACGTGAATTGATTGCCACTGCCAAATTAATTGCCGAAGCATCAGAAGATGTAACA
CGTATTGCTAAGGCATTGGCTAGAGAATGTACTGACAAGAGAATTAGAACAAATTTGCTA
CAAGTTTGTGAAAGAATACCAACAATTGGAACACAACTTAAAATTTTGTCAACAGTCAAA
GCAACAATGTTGGGTGCTCAAGGAAGCGATGAAGACCGTGAAGCAACAGAAATGCTTGTT
GGAAATGCTCAAAATCTCATGCAAAGCGTGAAAGAGACAGTTCGTGCCGCAGAAGGTGCT
AGTATTAAGATAAGAAGCGATCAAACAAATCATCGTCTGAGATGGATTCGTAGACAACCC
TGGCATGAGAGAATCGATCTTTCTGACGGAACCCGAGATATAATTGAGTATAAGCAATCG
TACTAAAATGTATGTGCCAAAGTATGATGAGTCGTACTTATCATTAAAAATCAAACAAAA
AATATATATTCAAAAATTTTATGATAAATTTAAAAAAATAAACACACTTGTTGATTCTAA
TGTGAATAAGCAATGTGCAGCAGCTAAGATTAAAACACATCGAGTGTTTACTAAATAAAT
TTATTTTAACAGACAAATTTTTATTTGTTTTCTCCTCTTCTCTACATTATTAATAAAATG
AATTACAAATTAAACTTAGAAATGATGAATAAAATTTAACTTTACGGTGACATTGTTGTT
GAAATTAAATGTAATGAAAAAAAAACAATCAAAAAAATTTATAGAAACTTTATGGCTTTA
GGATTGTTTAAAAAAACATGAAAAATGAACATTTTTCTTCGTCCCTTAATAATAAACATT
AACTTTTTTTGTGTACACTAAATAGTTCTAATAGGTTCGAAACAAATTAAAAATGATGTT
TTTTGAAGGTAAAAAGTTAAATAAATAAAAATCTTTTAAAAATTTAATAAAAATTTGACT
TTTATTCATAATCACATAATCT
>g13030.t3 Gene=g13030 Length=194
MPTSNQPILLAAHGLHQEVRQWSSKDNEIIAAAKRMAVLMARLSELVHQDSKGSKRELIA
TAKLIAEASEDVTRIAKALARECTDKRIRTNLLQVCERIPTIGTQLKILSTVKATMLGAQ
GSDEDREATEMLVGNAQNLMQSVKETVRAAEGASIKIRSDQTNHRLRWIRRQPWHERIDL
SDGTRDIIEYKQSY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13030.t3 | Gene3D | G3DSA:1.20.120.230 | - | 1 | 176 | 0 |
| 2 | g13030.t3 | PANTHER | PTHR46180:SF1 | VINCULIN | 3 | 175 | 0 |
| 3 | g13030.t3 | PANTHER | PTHR46180 | VINCULIN | 3 | 175 | 0 |
| 6 | g13030.t3 | PRINTS | PR00806 | Vinculin signature | 27 | 44 | 0 |
| 5 | g13030.t3 | PRINTS | PR00806 | Vinculin signature | 63 | 78 | 0 |
| 7 | g13030.t3 | PRINTS | PR00806 | Vinculin signature | 78 | 93 | 0 |
| 4 | g13030.t3 | PRINTS | PR00806 | Vinculin signature | 97 | 118 | 0 |
| 8 | g13030.t3 | PRINTS | PR00806 | Vinculin signature | 132 | 151 | 0 |
| 1 | g13030.t3 | Pfam | PF01044 | Vinculin family | 4 | 175 | 0 |
| 9 | g13030.t3 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 4 | 170 | 0 |
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.
