Gene loci information

Transcript annotation

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

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.t11 TTS g13384.t11 29619487 29619487
chr_1 g13384 g13384.t11 isoform g13384.t11 29620442 29621850
chr_1 g13384 g13384.t11 exon g13384.t11.exon1 29620442 29620785
chr_1 g13384 g13384.t11 cds g13384.t11.CDS1 29620444 29620785
chr_1 g13384 g13384.t11 exon g13384.t11.exon2 29620852 29621086
chr_1 g13384 g13384.t11 cds g13384.t11.CDS2 29620852 29621086
chr_1 g13384 g13384.t11 exon g13384.t11.exon3 29621146 29621284
chr_1 g13384 g13384.t11 cds g13384.t11.CDS3 29621146 29621284
chr_1 g13384 g13384.t11 exon g13384.t11.exon4 29621346 29621509
chr_1 g13384 g13384.t11 cds g13384.t11.CDS4 29621346 29621481
chr_1 g13384 g13384.t11 exon g13384.t11.exon5 29621708 29621850
chr_1 g13384 g13384.t11 TSS g13384.t11 29621850 29621850

Sequences

>g13384.t11 Gene=g13384 Length=1025
ACAACAACAACATTGAAAATAATAAAATTGTGCAAAAAATTTATAAATTTGAGAAAAATA
GCATTAAAATCAAATATCGACACTTTATTATCCTTCATTTGTTAAAATAACAACAATTGC
TGCTTAAGTGACAGTAAAACAAGAAGTTGGATCAAAAATCAATAACTTATAATGGCTGCT
GGAACAACTTTACAAAAAGCTATTGATATAGTAACGAAAGCAACAGAGGAAGATAGAAAT
AAAAATTATGAGGAAGCATTAAGGCTATATGAGCATGGTGTTGAATATTTTCTTCACGCT
ATTAAATACGAAGCTCAAGGTGACAAAGCAAAAGAATCGATTAGAGCAAAATGTTTACAG
TATCTTGATCGTGCAGAGAAACTCAAACAATATTTGAAAAAAGGAAAAAAGCAGAAACCT
GTAAAAGATGGAGATACAGGTTCCAAAGATAAAGATAAGAAAAGTGATAGTGATTCAGAT
GAAGATGATCCAGAGAAAAAGAAACTTCAGAGTAAATTGGAAGGCGCAATTGTTGTTGAG
AAACCTAAGGTTAAATGGTCAGATGTAGCCGGTCTCGAAGGCGCTAAGGAAGCGCTTAAA
GAAGCAGTCATTCTGCCAATAAAATTTCCTCATTTATTTACTGGAAAAAGAGTTCCATGG
AAAGGAATTTTACTCTTTGGGCCACCAGGTACTGGTAAATCTTATTTGGCTAAAGCTGTT
GCAACAGAAGCAAATAATTCTACATTCTTCTCTGTATCGAGTGCTGATTTGGTTTCAAAA
TGGCTCGGTGAATCAGAAAAGCTCGTTAGAAATCTCTTTGACTTGGCTCGTGCTCACAAG
CCTAGTATCATCTTTATCGATGAAGTTGACTCTTTATGTTCTTCTCGTTCTGAAAACGAA
AGTGAAAGTGCCCGTCGTATCAAAACCGAATTTCTTGTTCAAATGCAAGGTGTAGGCAAT
GATAATGAAGGAATTCTCGTTCTTGGTGCGACAAATATTCCATGGGTTCTTGATTCTGCT
ATTAG

>g13384.t11 Gene=g13384 Length=284
MAAGTTLQKAIDIVTKATEEDRNKNYEEALRLYEHGVEYFLHAIKYEAQGDKAKESIRAK
CLQYLDRAEKLKQYLKKGKKQKPVKDGDTGSKDKDKKSDSDSDEDDPEKKKLQSKLEGAI
VVEKPKVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRVPWKGILLFGPPGTGKSYLA
KAVATEANNSTFFSVSSADLVSKWLGESEKLVRNLFDLARAHKPSIIFIDEVDSLCSSRS
ENESESARRIKTEFLVQMQGVGNDNEGILVLGATNIPWVLDSAI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13384.t11 CDD cd02678 MIT_VPS4 6 75 2.70514E-36
13 g13384.t11 CDD cd00009 AAA 133 281 6.0321E-24
12 g13384.t11 Gene3D G3DSA:1.20.58.280 Hypothetical protein 1500032h18. 2 86 2.8E-34
11 g13384.t11 Gene3D G3DSA:3.40.50.300 - 119 284 1.0E-64
10 g13384.t11 MobiDBLite mobidb-lite consensus disorder prediction 76 112 -
9 g13384.t11 MobiDBLite mobidb-lite consensus disorder prediction 80 112 -
3 g13384.t11 PANTHER PTHR23074:SF72 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B 6 284 2.7E-118
4 g13384.t11 PANTHER PTHR23074 AAA DOMAIN-CONTAINING 6 284 2.7E-118
2 g13384.t11 Pfam PF04212 MIT (microtubule interacting and transport) domain 7 73 1.8E-23
1 g13384.t11 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 166 284 2.0E-36
8 g13384.t11 SMART SM00745 smart 3 82 2.5E-25
7 g13384.t11 SMART SM00382 AAA_5 162 282 6.2E-11
6 g13384.t11 SUPERFAMILY SSF116846 MIT domain 5 86 5.1E-28
5 g13384.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 121 283 2.67E-42

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