General information for g13384.t6
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.t6 | TTS | g13384.t6 | 29619487 | 29619487 |
| chr_1 | g13384 | g13384.t6 | isoform | g13384.t6 | 29619496 | 29621086 |
| chr_1 | g13384 | g13384.t6 | exon | g13384.t6.exon1 | 29619496 | 29620015 |
| chr_1 | g13384 | g13384.t6 | cds | g13384.t6.CDS1 | 29619914 | 29620015 |
| chr_1 | g13384 | g13384.t6 | exon | g13384.t6.exon2 | 29620075 | 29620785 |
| chr_1 | g13384 | g13384.t6 | cds | g13384.t6.CDS2 | 29620075 | 29620524 |
| chr_1 | g13384 | g13384.t6 | exon | g13384.t6.exon3 | 29620852 | 29621086 |
| chr_1 | g13384 | g13384.t6 | TSS | g13384.t6 | 29621850 | 29621850 |
Sequences
>g13384.t6 Gene=g13384 Length=1466
AGATAAAGATAAGAAAAGTGATAGTGATTCAGATGAAGATGATCCAGAGAAAAAGAAACT
TCAGAGTAAATTGGAAGGCGCAATTGTTGTTGAGAAACCTAAGGTTAAATGGTCAGATGT
AGCCGGTCTCGAAGGCGCTAAGGAAGCGCTTAAAGAAGCAGTCATTCTGCCAATAAAATT
TCCTCATTTATTTACTGGAAAAAGAGTTCCATGGAAAGGAATTTTACTCTTTGGGCCACC
AGGTACTGGTAAATCTTATTTGGCTAAAGCTGTTGCAACAGAAGCAAATAATTCTACATT
CTTCTCTGTATCGAGTGCTGATTTGGTTTCAAAATGGCTCGGTGAATCAGAAAAGCTCGT
TAGAAATCTCTTTGACTTGGCTCGTGCTCACAAGCCTAGTATCATCTTTATCGATGAAGT
TGACTCTTTATGTTCTTCTCGTTCTGAAAACGAAAGTGAAAGTGCCCGTCGTATCAAAAC
CGAATTTCTTGTTCAAATGCAAGGTGTAGGCAATGATAATGAAGGAATTCTCGTTCTTGG
TGCGACAAATATTCCATGGGTTCTTGATTCTGCTATTAGAAGACGTTTTGAAAAAAGAAT
TTATATACCTTTGCCTGAAGAAAACGCTCGCTTGGTCATGTTTAAAATTCATTTGGGCAA
CACATCGCATGTATTGACAGAAGAAAATTTAAGACAACTCGCAAAACAAACTGAAGGTTA
TTCAGGTGCTGATATTTCAATTGTAGTCCGTGATGCTCTTATGCAACCTGTTCGAAAAGT
TCAGACAGCAACACATTTTAAAAGGATTCGCGGTCCATCGCCTTTGGATAAAAATGTAAT
GGTAGATGATCTTCTTACACCTTGCTCGCCTGGTGAAAAAGGAGCAATTGAAATGACTTG
GATGGAAGTTGAGGGAGAGAAACTTTTTGAACCTCCAGTAACAATGGGTGACATGCTTAA
TTCACTTGCAAGAACAAAACCAACAATCAATGAAGACGATATGAAGAAACTGCAAAAGTT
CACTGACGATTTTGGTCAGGAGGGTTAAAAAATTGTACGGAATTCAACTATTTTCTATTT
AAATATTATATATTGCGAGAGTAAAATGTGCATGAGAAGAAGAACGTTGCCTATATTTAA
ACATACATACTTTTAGATATGATGAAAAGTTATTTCATTCACAATAAGCGATGATGATGA
TGAAGTTGATTTTACGCATACATGTCTCGTGATGAAATATGCTATTAATATTAATATAAC
CCAAGAGAGAAATACAAAGTTTTATTATACAGAAAAACCGGATTTTTCATACCAACTCTG
AAACAATATGGAATTTTTTACTTAACAGATTCAAATCACACAGAAAAATTAAGTAATCAA
ATGACTAATTTTTAATATCTTTTCTTCTCTGTTTGTTCTTAAAAAATAATTGATGTTGCG
TTTAAAAAGAAATAAAGTAAAAAAAT
>g13384.t6 Gene=g13384 Length=183
MQGVGNDNEGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEENARLVMFKIHLGNTSHVL
TEENLRQLAKQTEGYSGADISIVVRDALMQPVRKVQTATHFKRIRGPSPLDKNVMVDDLL
TPCSPGEKGAIEMTWMEVEGEKLFEPPVTMGDMLNSLARTKPTINEDDMKKLQKFTDDFG
QEG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13384.t6 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 172 | 1.3E-64 |
| 9 | g13384.t6 | Gene3D | G3DSA:1.10.8.60 | - | 40 | 162 | 1.3E-64 |
| 4 | g13384.t6 | PANTHER | PTHR23074:SF72 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B | 1 | 181 | 1.7E-68 |
| 5 | g13384.t6 | PANTHER | PTHR23074 | AAA DOMAIN-CONTAINING | 1 | 181 | 1.7E-68 |
| 2 | g13384.t6 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 1 | 39 | 9.9E-5 |
| 3 | g13384.t6 | Pfam | PF17862 | AAA+ lid domain | 64 | 97 | 1.3E-9 |
| 1 | g13384.t6 | Pfam | PF09336 | Vps4 C terminal oligomerisation domain | 120 | 180 | 4.8E-28 |
| 7 | g13384.t6 | ProSitePatterns | PS00674 | AAA-protein family signature. | 11 | 30 | - |
| 6 | g13384.t6 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 7 | 177 | 6.84E-19 |
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:0005524 | ATP binding | MF |
| GO:0016887 | ATP hydrolysis 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.
