Gene loci information

Transcript annotation

  • This transcript has been annotated as Vacuolar protein sorting-associated protein 41-like protein.

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 g13494 g13494.t3 TSS g13494.t3 30507623 30507623
chr_1 g13494 g13494.t3 isoform g13494.t3 30507726 30510320
chr_1 g13494 g13494.t3 exon g13494.t3.exon1 30507726 30507998
chr_1 g13494 g13494.t3 cds g13494.t3.CDS1 30507726 30507998
chr_1 g13494 g13494.t3 exon g13494.t3.exon2 30508061 30508725
chr_1 g13494 g13494.t3 cds g13494.t3.CDS2 30508061 30508725
chr_1 g13494 g13494.t3 exon g13494.t3.exon3 30508785 30508925
chr_1 g13494 g13494.t3 cds g13494.t3.CDS3 30508785 30508925
chr_1 g13494 g13494.t3 exon g13494.t3.exon4 30510318 30510320
chr_1 g13494 g13494.t3 cds g13494.t3.CDS4 30510318 30510318
chr_1 g13494 g13494.t3 TTS g13494.t3 30510719 30510719

Sequences

>g13494.t3 Gene=g13494 Length=1082
ATGGAGAATGATAAGACACAAGTCGAACCAATCTTCAAATATATAAGAATCGCATCAGAT
TTGCGAGAAATTTTAAAAAGTGACTCAATTTCAGTTTGTTTTCCAACATCAAAAATTCTT
TTTATTGGTTCAGGATGGGGAGTTCTTTATGTTTTAGATCATGAAGGAAATGCAATAAGT
GAACAAAAATTTCCCAAACACATGGTATCAATAAATATGATATCAGTGGACTCAAAAGGA
GAATATATTGCGACATGTAGTGATGATGGAAAAATTCACATAAACTGCCTCTATTCGCTT
GACAATAGTGTTTATTTGAATTTAGAAAAACAAGTAAAATGTATTGAACTTGATCCTGAT
TATGGAAGATCAAGTGGAAAAAGATTTATTGTTGGTGACCATCAATTGAAATTATATGAA
AAGACATTGCTGAGAGGAATTAAACCAACAGTTCTATGTGATTCTGAAGGAAATGTAAAT
GCATTGAAATGGAGTGATGGTGGTCAGTTTATTGCATGGGCAAATGCTATTGGAGTGAGA
GTTTATGATCTAGTCGAAAAATGTTCACTTGGACTGATAAGATGGGAAGAGCCACAAGAA
GCAAAATTATCTGATTTTCGATGCAATCTACTTTGGAATAATACAACACTTTTTATTGGT
TGGGCTGAAACGATAAGAATCTGTGTGATAAGAAAAAGAAGTGTTCTTGAATTATCAGCA
AGAAATTTGCCTGGCTACATTGTCGATCCAATTTCAACATTCAAGACCGAATTTTATATA
TGTGGTCTTGCGCCTTTAGAAAAAAATCAACTTGTTGTACTCGGATTACCAAAAGAAAAA
GAGAGCGATAATAAATCTCAAAGACCTGTACTATGTGTCATTCAATATAAATCAAATGAA
TATGAGGAATTATGCACTGATAGCTTGACATTAAAAGATTACGAATTTTACACACCAAAT
GACTACAGCTTAGGATGCTTAATTGATGAGAATAAATATTTTGTTATTTCACCAAAAGAT
ATTGTTGCTGCTTCACTTTATGAAACGGATGATCGTGTTAAATATCTCATCGAGCATGAT
CT

>g13494.t3 Gene=g13494 Length=360
MENDKTQVEPIFKYIRIASDLREILKSDSISVCFPTSKILFIGSGWGVLYVLDHEGNAIS
EQKFPKHMVSINMISVDSKGEYIATCSDDGKIHINCLYSLDNSVYLNLEKQVKCIELDPD
YGRSSGKRFIVGDHQLKLYEKTLLRGIKPTVLCDSEGNVNALKWSDGGQFIAWANAIGVR
VYDLVEKCSLGLIRWEEPQEAKLSDFRCNLLWNNTTLFIGWAETIRICVIRKRSVLELSA
RNLPGYIVDPISTFKTEFYICGLAPLEKNQLVVLGLPKEKESDNKSQRPVLCVIQYKSNE
YEELCTDSLTLKDYEFYTPNDYSLGCLIDENKYFVISPKDIVAASLYETDDRVKYLIEHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g13494.t3 Gene3D G3DSA:2.130.10.10 - 6 204 0.00
1 g13494.t3 PANTHER PTHR12616:SF1 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG 4 359 0.00
2 g13494.t3 PANTHER PTHR12616 VACUOLAR PROTEIN SORTING VPS41 4 359 0.00
4 g13494.t3 SMART SM00320 WD40_4 57 96 0.61
5 g13494.t3 SMART SM00320 WD40_4 145 183 37.00
3 g13494.t3 SUPERFAMILY SSF69322 Tricorn protease domain 2 34 270 0.00

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:0005515 protein binding MF

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.

Raw TPM values