General information for g13384.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 4B.
Parent gene
- The parent gene g13384 is located on chr_1: 29620442..29621850 (- 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 | g13384 | g13384.t2 | TTS | g13384.t2 | 29619487 | 29619487 |
| chr_1 | g13384 | g13384.t2 | isoform | g13384.t2 | 29619496 | 29620442 |
| chr_1 | g13384 | g13384.t2 | exon | g13384.t2.exon1 | 29619496 | 29619805 |
| chr_1 | g13384 | g13384.t2 | exon | g13384.t2.exon2 | 29619862 | 29620015 |
| chr_1 | g13384 | g13384.t2 | cds | g13384.t2.CDS1 | 29619914 | 29620015 |
| chr_1 | g13384 | g13384.t2 | exon | g13384.t2.exon3 | 29620075 | 29620442 |
| chr_1 | g13384 | g13384.t2 | cds | g13384.t2.CDS2 | 29620075 | 29620383 |
| chr_1 | g13384 | g13384.t2 | TSS | g13384.t2 | NA | NA |
Sequences
>g13384.t2 Gene=g13384 Length=832
GAAGACGTTTTGAAAAAAGAATTTATATACCTTTGCCTGAAGAAAACGCTCGCTTGGTCA
TGTTTAAAATTCATTTGGGCAACACATCGCATGTATTGACAGAAGAAAATTTAAGACAAC
TCGCAAAACAAACTGAAGGTTATTCAGGTGCTGATATTTCAATTGTAGTCCGTGATGCTC
TTATGCAACCTGTTCGAAAAGTTCAGACAGCAACACATTTTAAAAGGATTCGCGGTCCAT
CGCCTTTGGATAAAAATGTAATGGTAGATGATCTTCTTACACCTTGCTCGCCTGGTGAAA
AAGGAGCAATTGAAATGACTTGGATGGAAGTTGAGGGAGAGAAACTTTTTGAACCTCCAG
TAACAATGGGTGACATGCTTAATTCACTTGCAAGAACAAAACCAACAATCAATGAAGACG
ATATGAAGAAACTGCAAAAGTTCACTGACGATTTTGGTCAGGAGGGTTAAAAAATTGTAC
GGAATTCAACTATTTTCTATTTAAATATTATATATTGCGAGAATATGATGAAAAGTTATT
TCATTCACAATAAGCGATGATGATGATGAAGTTGATTTTACGCATACATGTCTCGTGATG
AAATATGCTATTAATATTAATATAACCCAAGAGAGAAATACAAAGTTTTATTATACAGAA
AAACCGGATTTTTCATACCAACTCTGAAACAATATGGAATTTTTTACTTAACAGATTCAA
ATCACACAGAAAAATTAAGTAATCAAATGACTAATTTTTAATATCTTTTCTTCTCTGTTT
GTTCTTAAAAAATAATTGATGTTGCGTTTAAAAAGAAATAAAGTAAAAAAAT
>g13384.t2 Gene=g13384 Length=136
MFKIHLGNTSHVLTEENLRQLAKQTEGYSGADISIVVRDALMQPVRKVQTATHFKRIRGP
SPLDKNVMVDDLLTPCSPGEKGAIEMTWMEVEGEKLFEPPVTMGDMLNSLARTKPTINED
DMKKLQKFTDDFGQEG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13384.t2 | Gene3D | G3DSA:1.10.8.60 | - | 1 | 115 | 0 |
| 5 | g13384.t2 | Gene3D | G3DSA:3.40.50.300 | - | 116 | 125 | 0 |
| 3 | g13384.t2 | PANTHER | PTHR23074:SF72 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B | 1 | 134 | 0 |
| 4 | g13384.t2 | PANTHER | PTHR23074 | AAA DOMAIN-CONTAINING | 1 | 134 | 0 |
| 2 | g13384.t2 | Pfam | PF17862 | AAA+ lid domain | 17 | 50 | 0 |
| 1 | g13384.t2 | Pfam | PF09336 | Vps4 C terminal oligomerisation domain | 73 | 133 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
