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.t1 TSS g13494.t1 30507623 30507623
chr_1 g13494 g13494.t1 isoform g13494.t1 30507726 30511809
chr_1 g13494 g13494.t1 exon g13494.t1.exon1 30507726 30507998
chr_1 g13494 g13494.t1 cds g13494.t1.CDS1 30507726 30507998
chr_1 g13494 g13494.t1 exon g13494.t1.exon2 30508061 30508725
chr_1 g13494 g13494.t1 cds g13494.t1.CDS2 30508061 30508725
chr_1 g13494 g13494.t1 exon g13494.t1.exon3 30508785 30508925
chr_1 g13494 g13494.t1 cds g13494.t1.CDS3 30508785 30508925
chr_1 g13494 g13494.t1 exon g13494.t1.exon4 30509166 30510202
chr_1 g13494 g13494.t1 cds g13494.t1.CDS4 30509166 30510202
chr_1 g13494 g13494.t1 exon g13494.t1.exon5 30510254 30511473
chr_1 g13494 g13494.t1 cds g13494.t1.CDS5 30510254 30511473
chr_1 g13494 g13494.t1 exon g13494.t1.exon6 30511537 30511809
chr_1 g13494 g13494.t1 cds g13494.t1.CDS6 30511537 30511809
chr_1 g13494 g13494.t1 TTS g13494.t1 30511979 30511979

Sequences

>g13494.t1 Gene=g13494 Length=3609
ATGGAGAATGATAAGACACAAGTCGAACCAATCTTCAAATATATAAGAATCGCATCAGAT
TTGCGAGAAATTTTAAAAAGTGACTCAATTTCAGTTTGTTTTCCAACATCAAAAATTCTT
TTTATTGGTTCAGGATGGGGAGTTCTTTATGTTTTAGATCATGAAGGAAATGCAATAAGT
GAACAAAAATTTCCCAAACACATGGTATCAATAAATATGATATCAGTGGACTCAAAAGGA
GAATATATTGCGACATGTAGTGATGATGGAAAAATTCACATAAACTGCCTCTATTCGCTT
GACAATAGTGTTTATTTGAATTTAGAAAAACAAGTAAAATGTATTGAACTTGATCCTGAT
TATGGAAGATCAAGTGGAAAAAGATTTATTGTTGGTGACCATCAATTGAAATTATATGAA
AAGACATTGCTGAGAGGAATTAAACCAACAGTTCTATGTGATTCTGAAGGAAATGTAAAT
GCATTGAAATGGAGTGATGGTGGTCAGTTTATTGCATGGGCAAATGCTATTGGAGTGAGA
GTTTATGATCTAGTCGAAAAATGTTCACTTGGACTGATAAGATGGGAAGAGCCACAAGAA
GCAAAATTATCTGATTTTCGATGCAATCTACTTTGGAATAATACAACACTTTTTATTGGT
TGGGCTGAAACGATAAGAATCTGTGTGATAAGAAAAAGAAGTGTTCTTGAATTATCAGCA
AGAAATTTGCCTGGCTACATTGTCGATCCAATTTCAACATTCAAGACCGAATTTTATATA
TGTGGTCTTGCGCCTTTAGAAAAAAATCAACTTGTTGTACTCGGATTACCAAAAGAAAAA
GAGAGCGATAATAAATCTCAAAGACCTGTACTATGTGTCATTCAATATAAATCAAATGAA
TATGAGGAATTATGCACTGATAGCTTGACATTAAAAGATTACGAATTTTACACACCAAAT
GACTACAGCTTAGGATGCTTAATTGATGAGAATAAATATTTTGTTATTTCACCAAAAGAT
ATTGTTGCTGCTTCACTTTATGAAACGGATGATCGTGTTAAATATCTCATCGAGCATGAT
GAATATAAATGTGACATCAGTAAATTCCATGATAAAGTTGATGAAAATAATTATTTAATA
GTAGCATTAATTTTAACTGCCCCAAAAAATTTTGATAGAAGAAATGTAATGCGAGAAACA
TGGCTGAGTTTAAGACCGTGGCAATTAAATGATAGTTTTTATCAAAATCAAATAATTTAC
ATACCATCAGAACAGAATAATGGCTTTCTAAAGTTAGAAAGTGTACAACAACAAGAGAGT
AGTCTAAAAAATTATCAAAAATGGTTGATGAATAATCATAAAGGTTCAAATGTCAAAGTG
CCAAACTTGAAAATAAAAACATTATTCGCTATCGGCACAAAAGACCTCGATGATGAAACA
GCGAAAAGAATCAGAGCAGAAAATGATGTTTATAATGATTTGCTTCTGCTCGATGAACTC
AAAGACTCGTATAAGAATCTCACATTGAAGCTATTAAGTGCATTAGAAAAAGTCAACTAT
GTTACACCCAATTTCAAATATCTTCTCAAATGTGATGATGATTCATATGTGAAGTTAGAC
TATTTAGCATTAGATCTCATAGAATATACCAAAAAGCTAAAAGTCAAACAATTAGAAAAA
AATCTCGAATTATATTGGGGCTTCTTTAATGGTCGTGCGAATATAAAGAAATCGGGTCAG
TGGAAAGAAGTCAATTATAACTTGTGTGATCGTTATTTGCCCTATGCATTAGGCGGTGGC
TATGTAATATCAAAGAATCTCGTTTCATACATTGGCAATCATAGCACAATTTTAAATCGT
TATGAAAGTGAAGATATATCTTTAGGTACATGGCTTTCAACATTCAGAAATATTCATTGG
AGACATGATCCACGTTTTGACACAACTTATATTCCACGAAAATGCCAAAAATATCATATT
GTAATGCACAAAAGAACAATAACCGATATGCAAGAAATACATAAGGGAAATCATTGTTTT
AGTGAAGTAAAATATGATGAAAACAAAAAACCGTCTGAATATTTTTATGATTGGTCTCAA
TTACCATCAAAATGCTGTAGTGCATTATGTCAATTTCTTAAAATTTTCTTTAATAATACT
CTTGTTTCTATCTTTAATAGTCTATATGAGAAAGCACTGGATGTGATACGTGAAAAAGGT
GGAAAGTTTTCTATGACACAAGTGGCACGACTTTATGTTGATCATCTCTTGAAAGAACAA
AAATATGATGAAGCTGCAAAATTATGTCTCGATGTGTTTGGAAATAATGTAGCATTATGG
GAAGATGAAGTTTATAAATTCTTAAAAGCAAAACAACTCAGAGCGATAAGTTCTTACTTG
CCCCGAACTAGTGATTGTAAATTGAATCCACAAGTATATGAAATGGTGATGTATGAATAT
CTTCAATTTGACATACCAGGATTTTTAGAATTGATTAAAGAATGGCAACCGCATCTCTAT
AATACATCAGTAATAATCAATGTTATTCGTGGTGAATTTGATAAAGACAAAAAAATGGAT
AAGAAAGAAAAGAAAATTTTACTTGAAGCTCTTGCAATTCTTTATTCACATGAGCGAGAA
TATGACAAAGCAGTGACAATGTACATTAAATTAGAACACAAAGATGTCTTTCAATTAATT
AAAAATCATAAACTGTACAACGTTATTAAACCAATGATTGTTGATCTGATGAAATTAGAT
ACTGAAAAAGCCATCAATATTCTCCTCAGTCAAAATGATATTTCACCAGCTGAAATTGTT
GAAAAGTTAAAGAAAAGTGAGAATGAAATGTTCCTGTATCAGTATTTGGATGCCTTTAAG
AGAATTGATAGAGCAGGAAAATTTGATTGGGAATTACTTAATCTTTATACGAAATATGAT
CGAGATAAGATGCTACCATTGCTCAAAAGATCGTATGAATATCCTCTGCAAGATGCTTAT
GAATTATGTAAAGTAAATTTATTCTATCCTGAAATGGTATACTTGTTAGAAAGATTAGGA
AACACAAATGAAGCATTAGAAATTATTTTAAAGAAAATGGAAAATATTCGAATGGCGATA
AACTTTTGCTGTGAGCATGATGACAGGGAATTATGGGAACATTTAATTAGCGAAAGCTTT
GAAAAACCTGAAATTATTACTCTACTAATGGATGGAATTTCCGGTTATTCAATCTCTATT
GATCCACAAATGCTTATTGATCGACTTCATGAAGGACAAGAAATTCCAGAACTTAAAAAA
GCTCTCACAAAAATGCTAACGGGTTATAGCTTACAAGTATCAATACACGAAGGATGCAAT
CAAATTCTCAAAACAGATTATTTTGATGTTCATAATAAACTCATCAAACAACAAGGAAAG
GCAATGTACTTTGGAAGTCAAACAGTCTGCAGTCTCTGTCAACGAAGCATAGTCAATATA
AAGGATAGAAATTCCAATAAAACTCCTCCAGATATTATTGTTTTCAATTGCAAACACATT
TTCCATGAGTCATGTAAATTTGATCATGACTATTGTTCCATATGTATTCCAACAAAAGAA
GTCCCATAA

>g13494.t1 Gene=g13494 Length=1202
MENDKTQVEPIFKYIRIASDLREILKSDSISVCFPTSKILFIGSGWGVLYVLDHEGNAIS
EQKFPKHMVSINMISVDSKGEYIATCSDDGKIHINCLYSLDNSVYLNLEKQVKCIELDPD
YGRSSGKRFIVGDHQLKLYEKTLLRGIKPTVLCDSEGNVNALKWSDGGQFIAWANAIGVR
VYDLVEKCSLGLIRWEEPQEAKLSDFRCNLLWNNTTLFIGWAETIRICVIRKRSVLELSA
RNLPGYIVDPISTFKTEFYICGLAPLEKNQLVVLGLPKEKESDNKSQRPVLCVIQYKSNE
YEELCTDSLTLKDYEFYTPNDYSLGCLIDENKYFVISPKDIVAASLYETDDRVKYLIEHD
EYKCDISKFHDKVDENNYLIVALILTAPKNFDRRNVMRETWLSLRPWQLNDSFYQNQIIY
IPSEQNNGFLKLESVQQQESSLKNYQKWLMNNHKGSNVKVPNLKIKTLFAIGTKDLDDET
AKRIRAENDVYNDLLLLDELKDSYKNLTLKLLSALEKVNYVTPNFKYLLKCDDDSYVKLD
YLALDLIEYTKKLKVKQLEKNLELYWGFFNGRANIKKSGQWKEVNYNLCDRYLPYALGGG
YVISKNLVSYIGNHSTILNRYESEDISLGTWLSTFRNIHWRHDPRFDTTYIPRKCQKYHI
VMHKRTITDMQEIHKGNHCFSEVKYDENKKPSEYFYDWSQLPSKCCSALCQFLKIFFNNT
LVSIFNSLYEKALDVIREKGGKFSMTQVARLYVDHLLKEQKYDEAAKLCLDVFGNNVALW
EDEVYKFLKAKQLRAISSYLPRTSDCKLNPQVYEMVMYEYLQFDIPGFLELIKEWQPHLY
NTSVIINVIRGEFDKDKKMDKKEKKILLEALAILYSHEREYDKAVTMYIKLEHKDVFQLI
KNHKLYNVIKPMIVDLMKLDTEKAINILLSQNDISPAEIVEKLKKSENEMFLYQYLDAFK
RIDRAGKFDWELLNLYTKYDRDKMLPLLKRSYEYPLQDAYELCKVNLFYPEMVYLLERLG
NTNEALEIILKKMENIRMAINFCCEHDDRELWEHLISESFEKPEIITLLMDGISGYSISI
DPQMLIDRLHEGQEIPELKKALTKMLTGYSLQVSIHEGCNQILKTDYFDVHNKLIKQQGK
AMYFGSQTVCSLCQRSIVNIKDRNSNKTPPDIIVFNCKHIFHESCKFDHDYCSICIPTKE
VP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13494.t1 Coils Coil Coil 497 517 -
12 g13494.t1 Coils Coil Coil 1016 1036 -
11 g13494.t1 Gene3D G3DSA:2.130.10.10 - 6 201 2.6E-10
4 g13494.t1 PANTHER PTHR12616:SF1 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG 4 368 1.1E-194
6 g13494.t1 PANTHER PTHR12616 VACUOLAR PROTEIN SORTING VPS41 4 368 1.1E-194
3 g13494.t1 PANTHER PTHR12616:SF1 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG 728 1186 1.1E-194
5 g13494.t1 PANTHER PTHR12616 VACUOLAR PROTEIN SORTING VPS41 728 1186 1.1E-194
2 g13494.t1 Pfam PF01762 Galactosyltransferase 456 634 7.0E-27
1 g13494.t1 Pfam PF00637 Region in Clathrin and VPS 930 1064 9.5E-17
15 g13494.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 927 1068 20.375
14 g13494.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 1150 1195 8.535
9 g13494.t1 SMART SM00320 WD40_4 57 96 0.61
10 g13494.t1 SMART SM00320 WD40_4 145 183 37.0
8 g13494.t1 SMART SM00299 CLH_2 927 1068 1.2E-12
7 g13494.t1 SUPERFAMILY SSF69322 Tricorn protease domain 2 34 267 3.4E-16

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:0016020 membrane CC
GO:0006886 intracellular protein transport BP
GO:0006486 protein glycosylation BP
GO:0005515 protein binding MF
GO:0016758 hexosyltransferase activity MF
GO:0016192 vesicle-mediated 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.

Raw TPM values