Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vacuolar protein-sorting-associated protein 25.

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 g11814 g11814.t4 TSS g11814.t4 18530969 18530969
chr_1 g11814 g11814.t4 isoform g11814.t4 18531053 18531652
chr_1 g11814 g11814.t4 exon g11814.t4.exon1 18531053 18531108
chr_1 g11814 g11814.t4 cds g11814.t4.CDS1 18531053 18531108
chr_1 g11814 g11814.t4 exon g11814.t4.exon2 18531205 18531652
chr_1 g11814 g11814.t4 cds g11814.t4.CDS2 18531205 18531652
chr_1 g11814 g11814.t4 TTS g11814.t4 18531685 18531685

Sequences

>g11814.t4 Gene=g11814 Length=504
ATGACAGAATCAGAATTCGATTTTCCTTGGGAATACAATTTTCCTCCATTCTTTACAAAA
CAGCAATTTCTTCGTTGGAAGGAACTTATTTTAGCATATGCAAAACATAAAAATCAGGCG
ATTATTAATATAAATGATGAGTCTGAATTATTTCACAATAATAAAATCAATAGAACCTTA
GACAGAGAATCAAGGGAAATGATTTTAAATGAACTATGTAATTCAAGTAACGCAGCAAGA
GTGAACAAGAACACGGGAACTTATGAAATTTATTGGTTGACAATAGAAGAATGGTCAAAT
GTCATCTATACATATGCTTTAAACAGTGGAATGACTAATTCGGTGCTTACATTTTTTGAA
CTTCTTAATGGTGATGACAGTAAAGATCAAGAATTTCATCAGTTAAATGAACAAGTTTTT
ATGAAAGCTCTTAAACATTTGGAAACAAAAGGAAAATGTGAAATAATGGAAATAGATGGA
AGCTTTGGTGTAAAATTTTTTTAA

>g11814.t4 Gene=g11814 Length=167
MTESEFDFPWEYNFPPFFTKQQFLRWKELILAYAKHKNQAIININDESELFHNNKINRTL
DRESREMILNELCNSSNAARVNKNTGTYEIYWLTIEEWSNVIYTYALNSGMTNSVLTFFE
LLNGDDSKDQEFHQLNEQVFMKALKHLETKGKCEIMEIDGSFGVKFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11814.t4 Gene3D G3DSA:1.10.10.570 - 2 90 0
7 g11814.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 91 167 0
2 g11814.t4 PANTHER PTHR13149:SF0 VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 25 3 167 0
3 g11814.t4 PANTHER PTHR13149 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS25 3 167 0
1 g11814.t4 Pfam PF05871 ESCRT-II complex subunit 11 135 0
5 g11814.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 6 98 0
4 g11814.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 94 166 0

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:0071985 multivesicular body sorting pathway BP
GO:0000814 ESCRT II complex CC

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. There were no conditions that were differentially expressed