General information for g13494.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vacuolar protein sorting-associated protein 41-like protein.
Parent gene
- The parent gene g13494 is located on chr_1: 30510723..30511809 (+ 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 | g13494 | g13494.t2 | TSS | g13494.t2 | 30507623 | 30507623 |
| chr_1 | g13494 | g13494.t2 | isoform | g13494.t2 | 30507726 | 30508725 |
| chr_1 | g13494 | g13494.t2 | exon | g13494.t2.exon1 | 30507726 | 30507998 |
| chr_1 | g13494 | g13494.t2 | cds | g13494.t2.CDS1 | 30507726 | 30507998 |
| chr_1 | g13494 | g13494.t2 | exon | g13494.t2.exon2 | 30508061 | 30508725 |
| chr_1 | g13494 | g13494.t2 | cds | g13494.t2.CDS2 | 30508061 | 30508723 |
| chr_1 | g13494 | g13494.t2 | TTS | g13494.t2 | NA | NA |
Sequences
>g13494.t2 Gene=g13494 Length=938
ATGGAGAATGATAAGACACAAGTCGAACCAATCTTCAAATATATAAGAATCGCATCAGAT
TTGCGAGAAATTTTAAAAAGTGACTCAATTTCAGTTTGTTTTCCAACATCAAAAATTCTT
TTTATTGGTTCAGGATGGGGAGTTCTTTATGTTTTAGATCATGAAGGAAATGCAATAAGT
GAACAAAAATTTCCCAAACACATGGTATCAATAAATATGATATCAGTGGACTCAAAAGGA
GAATATATTGCGACATGTAGTGATGATGGAAAAATTCACATAAACTGCCTCTATTCGCTT
GACAATAGTGTTTATTTGAATTTAGAAAAACAAGTAAAATGTATTGAACTTGATCCTGAT
TATGGAAGATCAAGTGGAAAAAGATTTATTGTTGGTGACCATCAATTGAAATTATATGAA
AAGACATTGCTGAGAGGAATTAAACCAACAGTTCTATGTGATTCTGAAGGAAATGTAAAT
GCATTGAAATGGAGTGATGGTGGTCAGTTTATTGCATGGGCAAATGCTATTGGAGTGAGA
GTTTATGATCTAGTCGAAAAATGTTCACTTGGACTGATAAGATGGGAAGAGCCACAAGAA
GCAAAATTATCTGATTTTCGATGCAATCTACTTTGGAATAATACAACACTTTTTATTGGT
TGGGCTGAAACGATAAGAATCTGTGTGATAAGAAAAAGAAGTGTTCTTGAATTATCAGCA
AGAAATTTGCCTGGCTACATTGTCGATCCAATTTCAACATTCAAGACCGAATTTTATATA
TGTGGTCTTGCGCCTTTAGAAAAAAATCAACTTGTTGTACTCGGATTACCAAAAGAAAAA
GAGAGCGATAATAAATCTCAAAGACCTGTACTATGTGTCATTCAATATAAATCAAATGAA
TATGAGGAATTATGCACTGATAGCTTGACATTAAAAGA
>g13494.t2 Gene=g13494 Length=312
MENDKTQVEPIFKYIRIASDLREILKSDSISVCFPTSKILFIGSGWGVLYVLDHEGNAIS
EQKFPKHMVSINMISVDSKGEYIATCSDDGKIHINCLYSLDNSVYLNLEKQVKCIELDPD
YGRSSGKRFIVGDHQLKLYEKTLLRGIKPTVLCDSEGNVNALKWSDGGQFIAWANAIGVR
VYDLVEKCSLGLIRWEEPQEAKLSDFRCNLLWNNTTLFIGWAETIRICVIRKRSVLELSA
RNLPGYIVDPISTFKTEFYICGLAPLEKNQLVVLGLPKEKESDNKSQRPVLCVIQYKSNE
YEELCTDSLTLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13494.t2 | Gene3D | G3DSA:2.130.10.10 | - | 5 | 205 | 0.00 |
| 1 | g13494.t2 | PANTHER | PTHR12616:SF1 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG | 4 | 311 | 0.00 |
| 2 | g13494.t2 | PANTHER | PTHR12616 | VACUOLAR PROTEIN SORTING VPS41 | 4 | 311 | 0.00 |
| 4 | g13494.t2 | SMART | SM00320 | WD40_4 | 57 | 96 | 0.61 |
| 5 | g13494.t2 | SMART | SM00320 | WD40_4 | 145 | 183 | 37.00 |
| 3 | g13494.t2 | SUPERFAMILY | SSF69322 | Tricorn protease domain 2 | 34 | 265 | 0.00 |
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.
