Gene loci information

Transcript annotation

  • This transcript has been annotated as Vacuolar protein sorting-associated protein 26.

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_3 g2645 g2645.t8 TSS g2645.t8 19304175 19304175
chr_3 g2645 g2645.t8 isoform g2645.t8 19304257 19305697
chr_3 g2645 g2645.t8 exon g2645.t8.exon1 19304257 19304259
chr_3 g2645 g2645.t8 cds g2645.t8.CDS1 19304257 19304259
chr_3 g2645 g2645.t8 exon g2645.t8.exon2 19304317 19304463
chr_3 g2645 g2645.t8 cds g2645.t8.CDS2 19304317 19304463
chr_3 g2645 g2645.t8 exon g2645.t8.exon3 19304724 19304790
chr_3 g2645 g2645.t8 cds g2645.t8.CDS3 19304724 19304790
chr_3 g2645 g2645.t8 exon g2645.t8.exon4 19304862 19305027
chr_3 g2645 g2645.t8 cds g2645.t8.CDS4 19304862 19305027
chr_3 g2645 g2645.t8 exon g2645.t8.exon5 19305101 19305366
chr_3 g2645 g2645.t8 cds g2645.t8.CDS5 19305101 19305366
chr_3 g2645 g2645.t8 exon g2645.t8.exon6 19305448 19305697
chr_3 g2645 g2645.t8 cds g2645.t8.CDS6 19305448 19305695
chr_3 g2645 g2645.t8 TTS g2645.t8 19306293 19306293

Sequences

>g2645.t8 Gene=g2645 Length=899
ATGAACTTTCTGGGATTCGGGCAAACAGCAGATATTGATGTAGTTTTTGCGGACAGTGAA
AACAGAAAATATGCTGATTGTCGAATGGACGAGAATGGAAAAAAGGAAAAATTATTACTC
TATTATGATGGAGAAACGATTTCGGGAAAGGTCAACGTAACGTTAAAGAAACCAGGCACT
AAGCTTGAACATCAGGGAATAAAAATCGAATTGATAGGCCAAATTGAATTATTCTATGAT
CGCGGAAATCATCATGAATTTTTGACACAGCTCAAAGAGCTTGCACGTCATGGTGATCTT
ATTAAAAACACCAGCTATCCATTTGAATTTCCAAATGTAGAAAAGCCGTATGAAGTGTAT
ACGGGCTCTAATGTTCGATTGAGATATTTTCTTCGTGTGACAATTGTTCGACGAATCAGT
GATATTGTACGTGAAATCGATATTGCTGTTCATACATTAAGCAGCTATCCGGAAATGAAT
AGTCCGATCAAAATGGAAGTTGGAATTGAAGACTGCCTTCACATAGAATTTGAGTACAAC
AAGAGCAAATATCATCTAAAAGATGTCATTGTGGGAAAAATTTATTTTTTGTTGGTTCGC
ATCAAAATTAAGCATATGGAAATAGCTATAATTAAGAGAGAGACAACTGGTTCAAATGTT
TTTACTGAAAATGAAACTATAGCAAAATATGAGATTATGGATGGAGCTCCCGTCAAAGGC
GAAAGTATTCCGATTCGTGTATTTTTAGCTGGCTACGATTTGACGCCAACAATGAGGGAC
ATTAATAAGAAATTTTCTGTTCGCTATTTTCTCAATTTAGTCCTAATGGATACTGAAGAT
CGACGTTATTTTAAACAACAGGAGATCACATTATGGCGTAAGTCAGAAAAGACAAGAAA

>g2645.t8 Gene=g2645 Length=299
MNFLGFGQTADIDVVFADSENRKYADCRMDENGKKEKLLLYYDGETISGKVNVTLKKPGT
KLEHQGIKIELIGQIELFYDRGNHHEFLTQLKELARHGDLIKNTSYPFEFPNVEKPYEVY
TGSNVRLRYFLRVTIVRRISDIVREIDIAVHTLSSYPEMNSPIKMEVGIEDCLHIEFEYN
KSKYHLKDVIVGKIYFLLVRIKIKHMEIAIIKRETTGSNVFTENETIAKYEIMDGAPVKG
ESIPIRVFLAGYDLTPTMRDINKKFSVRYFLNLVLMDTEDRRYFKQQEITLWRKSEKTR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2645.t8 Gene3D G3DSA:2.60.40.640 - 1 155 0.0e+00
5 g2645.t8 Gene3D G3DSA:2.60.40.640 - 156 299 0.0e+00
2 g2645.t8 PANTHER PTHR12233:SF1 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26 1 296 0.0e+00
3 g2645.t8 PANTHER PTHR12233 VACUOLAR PROTEIN SORTING 26 RELATED 1 296 0.0e+00
1 g2645.t8 Pfam PF03643 Vacuolar protein sorting-associated protein 26 6 280 0.0e+00
4 g2645.t8 SUPERFAMILY SSF81296 E set domains 40 160 9.8e-06

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:0006886 intracellular protein transport BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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