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.t9 TTS g13384.t9 29619487 29619487
chr_1 g13384 g13384.t9 isoform g13384.t9 29619914 29621481
chr_1 g13384 g13384.t9 exon g13384.t9.exon1 29619914 29620778
chr_1 g13384 g13384.t9 cds g13384.t9.CDS1 29620045 29620778
chr_1 g13384 g13384.t9 exon g13384.t9.exon2 29620852 29621481
chr_1 g13384 g13384.t9 cds g13384.t9.CDS2 29620852 29620876
chr_1 g13384 g13384.t9 TSS g13384.t9 29621850 29621850

Sequences

>g13384.t9 Gene=g13384 Length=1495
ATGGCTGCTGGAACAACTTTACAAAAAGCTATTGATATAGTAACGAAAGCAACAGAGGAA
GATAGAAATAAAAATTATGAGGAAGCATTAAGGCTATATGAGCATGGTGTTGAATATTTT
CTTCACGCTATTAAATGTAAGTTAATTTAATATTTGATGTTCAACAAAATAATAAATTGC
GATTTCATTTTTTTTAGACGAAGCTCAAGGTGACAAAGCAAAAGAATCGATTAGAGCAAA
ATGTTTACAGTATCTTGATCGTGCAGAGAAACTCAAACAATATTTGAAAAAAGGAAAAAA
GCAGAAACCTGTAAAAGATGGAGATACAGGTTCCAAGTAATTAAACTATTCCTTCTAATA
AGTGTTAATTTAATTAAAATTATTTCTTATTATAGAGATAAAGATAAGAAAAGTGATAGT
GATTCAGATGAAGATGATCCAGAGAAAAAGAAACTTCAGAGTAAATTGGAAGGCGCAATT
GTTGTTGAGAAACCTAAGGTTAAATGGTCAGATGTAGCCGGTCTCGAAGGCGCTAAGGAA
GCGCTTAAAGAAGCAGTCATTCTGCCAATAAAATTTCCTCATTTATTTACTGGAAAAAGA
GTTCCATGGAAAGGAATTTTACTCTTTGGGGTACTGGTAAATCTTATTTGGCTAAAGCTG
TTGCAACAGAAGCAAATAATTCTACATTCTTCTCTGTATCGAGTGCTGATTTGGTTTCAA
AATGGCTCGGTGAATCAGAAAAGCTCGTTAGAAATCTCTTTGACTTGGCTCGTGCTCACA
AGCCTAGTATCATCTTTATCGATGAAGTTGACTCTTTATGTTCTTCTCGTTCTGAAAACG
AAAGTGAAAGTGCCCGTCGTATCAAAACCGAATTTCTTGTTCAAATGCAAGGTGTAGGCA
ATGATAATGAAGGAATTCTCGTTCTTGGTGCGACAAATATTCCATGGGTTCTTGATTCTG
CTATTAGAAGACGTTTTGAAAAAAGAATTTATATACCTTTGCCTGAAGAAAACGCTCGCT
TGGTCATGTTTAAAATTCATTTGGGCAACACATCGCATGTATTGACAGAAGAAAATTTAA
GACAACTCGCAAAACAAACTGAAGGTTATTCAGGTGCTGATATTTCAATTGTAGTCCGTG
ATGCTCTTATGCAACCTGTTCGAAAAGTTCAGACAGCAACACATTTTAAAAGGATTCGCG
GTCCATCGCCTTTGGATAAAAATGTAATGGTAGATGATCTTCTTACACCTTGCTCGCCTG
GTGAAAAAGGAGCAATTGAAATGACTTGGATGGAAGTTGAGGGAGAGAAACTTTTTGAAC
CTCCAGTAACAATGGTAATGGTATCATTTTATTTAAGTATTTAAGAAATAAAAAAGTATT
TTTTTTTTCATAGGGTGACATGCTTAATTCACTTGCAAGAACAAAACCAACAATCAATGA
AGACGATATGAAGAAACTGCAAAAGTTCACTGACGATTTTGGTCAGGAGGGTTAA

>g13384.t9 Gene=g13384 Length=252
MERNFTLWGTGKSYLAKAVATEANNSTFFSVSSADLVSKWLGESEKLVRNLFDLARAHKP
SIIFIDEVDSLCSSRSENESESARRIKTEFLVQMQGVGNDNEGILVLGATNIPWVLDSAI
RRRFEKRIYIPLPEENARLVMFKIHLGNTSHVLTEENLRQLAKQTEGYSGADISIVVRDA
LMQPVRKVQTATHFKRIRGPSPLDKNVMVDDLLTPCSPGEKGAIEMTWMEVEGEKLFEPP
VTMVMVSFYLSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13384.t9 CDD cd00009 AAA 9 132 7.05344E-20
9 g13384.t9 Gene3D G3DSA:3.40.50.300 - 7 131 3.0E-43
10 g13384.t9 Gene3D G3DSA:1.10.8.60 - 132 251 8.9E-34
4 g13384.t9 PANTHER PTHR23074:SF72 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B 9 244 1.4E-112
5 g13384.t9 PANTHER PTHR23074 AAA DOMAIN-CONTAINING 9 244 1.4E-112
2 g13384.t9 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 9 132 1.3E-36
3 g13384.t9 Pfam PF17862 AAA+ lid domain 157 190 2.1E-9
1 g13384.t9 Pfam PF09336 Vps4 C terminal oligomerisation domain 213 243 3.9E-12
8 g13384.t9 ProSitePatterns PS00674 AAA-protein family signature. 104 123 -
7 g13384.t9 SMART SM00382 AAA_5 2 134 2.3E-10
6 g13384.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 9 190 5.34E-44

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