Gene loci information

Transcript annotation

  • This transcript has been annotated as Vacuolar protein sorting-associated protein 4B.

Parent gene

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.t5 TTS g13384.t5 29619487 29619487
chr_1 g13384 g13384.t5 isoform g13384.t5 29619496 29620861
chr_1 g13384 g13384.t5 exon g13384.t5.exon1 29619496 29620015
chr_1 g13384 g13384.t5 cds g13384.t5.CDS1 29619914 29620015
chr_1 g13384 g13384.t5 exon g13384.t5.exon2 29620069 29620785
chr_1 g13384 g13384.t5 cds g13384.t5.CDS2 29620069 29620524
chr_1 g13384 g13384.t5 exon g13384.t5.exon3 29620852 29620861
chr_1 g13384 g13384.t5 TSS g13384.t5 29621850 29621850

Sequences

>g13384.t5 Gene=g13384 Length=1247
ACTCTTTGGGCCACCAGGTACTGGTAAATCTTATTTGGCTAAAGCTGTTGCAACAGAAGC
AAATAATTCTACATTCTTCTCTGTATCGAGTGCTGATTTGGTTTCAAAATGGCTCGGTGA
ATCAGAAAAGCTCGTTAGAAATCTCTTTGACTTGGCTCGTGCTCACAAGCCTAGTATCAT
CTTTATCGATGAAGTTGACTCTTTATGTTCTTCTCGTTCTGAAAACGAAAGTGAAAGTGC
CCGTCGTATCAAAACCGAATTTCTTGTTCAAATGCAAGGTGTAGGCAATGATAATGAAGG
AATTCTCGTTCTTGGTGCGACAAATATTCCATGGGTTCTTGATTCTGCTATTAGAAGACG
TTTTGAAAAAAGAATTTATATACCTTTGCCTGAAGAAAACGCTCGCTTGGTCATGTTTAA
AATTCATTTGGGCAACACATCGCATGTATTGACAGAAGAAAATTTAAGACAACTCGCAAA
ACAAACTGAAGGTTATTCAGGTGCTGATATTTCAATTGTAGTCCGTGATGCTCTTATGCA
ACCTGTTCGAAAAGTTCAGACAGCAACACATTTTAAAAGGATTCGCGGTCCATCGCCTTT
GGATAAAAATGTAATGGTAGATGATCTTCTTACACCTTGCTCGCCTGGTGAAAAAGGAGC
AATTGAAATGACTTGGATGGAAGTTGAGGGAGAGAAACTTTTTGAACCTCCAGTAACAAT
GGTAATGGGTGACATGCTTAATTCACTTGCAAGAACAAAACCAACAATCAATGAAGACGA
TATGAAGAAACTGCAAAAGTTCACTGACGATTTTGGTCAGGAGGGTTAAAAAATTGTACG
GAATTCAACTATTTTCTATTTAAATATTATATATTGCGAGAGTAAAATGTGCATGAGAAG
AAGAACGTTGCCTATATTTAAACATACATACTTTTAGATATGATGAAAAGTTATTTCATT
CACAATAAGCGATGATGATGATGAAGTTGATTTTACGCATACATGTCTCGTGATGAAATA
TGCTATTAATATTAATATAACCCAAGAGAGAAATACAAAGTTTTATTATACAGAAAAACC
GGATTTTTCATACCAACTCTGAAACAATATGGAATTTTTTACTTAACAGATTCAAATCAC
ACAGAAAAATTAAGTAATCAAATGACTAATTTTTAATATCTTTTCTTCTCTGTTTGTTCT
TAAAAAATAATTGATGTTGCGTTTAAAAAGAAATAAAGTAAAAAAAT

>g13384.t5 Gene=g13384 Length=185
MQGVGNDNEGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEENARLVMFKIHLGNTSHVL
TEENLRQLAKQTEGYSGADISIVVRDALMQPVRKVQTATHFKRIRGPSPLDKNVMVDDLL
TPCSPGEKGAIEMTWMEVEGEKLFEPPVTMVMGDMLNSLARTKPTINEDDMKKLQKFTDD
FGQEG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13384.t5 Gene3D G3DSA:3.40.50.300 - 1 174 1.8E-62
9 g13384.t5 Gene3D G3DSA:1.10.8.60 - 40 164 1.8E-62
4 g13384.t5 PANTHER PTHR23074:SF72 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B 1 183 4.5E-67
5 g13384.t5 PANTHER PTHR23074 AAA DOMAIN-CONTAINING 1 183 4.5E-67
2 g13384.t5 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 1 39 1.0E-4
3 g13384.t5 Pfam PF17862 AAA+ lid domain 64 97 1.3E-9
1 g13384.t5 Pfam PF09336 Vps4 C terminal oligomerisation domain 120 182 1.6E-25
7 g13384.t5 ProSitePatterns PS00674 AAA-protein family signature. 11 30 -
6 g13384.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 177 7.99E-18

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.

Raw TPM values