Gene loci information

Transcript annotation

  • This transcript has been annotated as Vacuolar protein sorting-associated protein 8-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 g13538 g13538.t1 isoform g13538.t1 30762966 30767125
chr_1 g13538 g13538.t1 exon g13538.t1.exon1 30762966 30764510
chr_1 g13538 g13538.t1 cds g13538.t1.CDS1 30762966 30764510
chr_1 g13538 g13538.t1 exon g13538.t1.exon2 30764571 30764792
chr_1 g13538 g13538.t1 cds g13538.t1.CDS2 30764571 30764792
chr_1 g13538 g13538.t1 exon g13538.t1.exon3 30764848 30765629
chr_1 g13538 g13538.t1 cds g13538.t1.CDS3 30764848 30765629
chr_1 g13538 g13538.t1 exon g13538.t1.exon4 30765695 30766637
chr_1 g13538 g13538.t1 cds g13538.t1.CDS4 30765695 30766637
chr_1 g13538 g13538.t1 exon g13538.t1.exon5 30766697 30766933
chr_1 g13538 g13538.t1 cds g13538.t1.CDS5 30766697 30766933
chr_1 g13538 g13538.t1 exon g13538.t1.exon6 30767024 30767125
chr_1 g13538 g13538.t1 cds g13538.t1.CDS6 30767024 30767125
chr_1 g13538 g13538.t1 TSS g13538.t1 30767191 30767191
chr_1 g13538 g13538.t1 TTS g13538.t1 NA NA

Sequences

>g13538.t1 Gene=g13538 Length=3831
ATGGACTCATTAAAAGCTCCGAGTTTAAGTTCATTAATATCAGGAACAGATCGTGGATCA
AGCGACTCACTTTTAGGATCAATAAACCTCGATTTAGATGATATTGATGATGATTTGTCG
CTTCCACCTACTGGTGAACTTCCTTCACTTGATACTGTGATGAATGAAATTGATAGTGAT
GTTGATATCGATAGCATAAACAATTTAGTTCCGGACAATAGAAAATTCTCCCAAACACCA
ACTTCGTCATTTCAAGAAGAAAAGCAACAGCATCAGACTGGTTCAATTTTAAGACATTTA
ATCTTTCAAGGAGTAACATCACAAATTGGATCGGCTGCTGATCGAATTGAGGCTGGATTT
GCATCAGCAATGTGTGTATCGAGAATGATTGCAATCGGTACTTCACATGGATTTATACTT
GCTTTTGATGCAGCTCAAACATTAAAATGGTGTTGTCAAGAAGGTCAAAAGAAGCAGCAA
GGTGCAGTTTCTTCGTTATCATTTAATTTAGATGATACACGATTATTGGCTGGTTTCTCT
CGCGGTGCAATATTGATGATAAATACACTGACTGGAGATGTGCTTAGAATTTTAACAGAA
TCTATTTCTCCAAATGCCGGTGTTTTAACTATTAAATGGACATCAAGACCAACACTTGCA
TTATCACTTGATTCTGGTGGTTCAGTATGGAGTTTATCATTTACTAGAAGAATGGGAATT
CGTGGATGCGATTCTAGATGCTTATTCAGTGGTGCAAGAGGAGAAGTTTGTACCTTTGAA
CCATTAATTGTAAATGATGAATCGCACCCTTTTCAAAATAATTATACATTGGTTGCATTA
GCAACACTCAGTAAATTTTTTATTCTCATGATTCGTCCACGACTAAAAGTCATTAAATAT
CATATGTTAAATGGACCTCCCGATAGTTTGCCATTACTTTCTTGGCAAATGGTGCTTATT
CAATCAGCCGATACTAGTCGAAGTGTTGATCCTGTTTTAGCTACTGGCAGAGCAAACTCA
CTTTATTTTCATCAAGTTACGTATCATAACGGTCGCATTAATGTAACTTTTCTTCGACAT
ATTACATTAGGCTACAATTTACTTTCACTTCACTGGCTTGGACCAAAGAACATTGCATGT
ATAGAACGTAATACTGAAATTCTTCATCTAATCGATGTGAGAACAAGTCGAGAACTGGAA
TCAATTGATGTTTCAAATTTCGGAATAATTTATTCATCAGCACAATTCAAAGGAATTGCA
ACTGGCGGGAATGTTTCTAAAGCTCTCGCTCTTGCTGGAACTTTTGCGTGCTATAGTACT
ATAGTGTCAAATGATTATAACTCAACACTATATATTTTGGGTAAAAGAAGCTTGCATGGA
ATAAATGCAAGAAGTTGGAGTGATCGATTAACATATTTGACAAATAAAAAGCAGTGGAAT
GAGGCATTTGACCTTGCAATTGATGCTTATAAGAGCACAACAGAAAAACCAAGAAGACAT
GTAATTACTAAAGAACGCATTTTACAACTGTTTGATGATTATCTCAATGGAACGACTCGA
TCTCCTGAATTATGTCTAGAGAGTGCAATCCGTTGTCTAATTGAAATTGATAGAACTGAT
TTATTGTGGCAAGAATTGTGGGATCGACTTTATTCTCAAGAAACTTATTTGAATTTGATC
ACACAGCATATTTTGAATGACGATTTGTCTCTCATATCACCAACTATTTCACAAGCGTTA
CTTGACTATTGGTCAAAAGTTTCTATAGAAAAATTAGAGGCTATAATTTTGAAACTCGAA
TGGCAGTGCCTTGATCTTCATCAAGCATTAAATTTTGTGAAAAATTTTCAACTATATAAG
GCACTTATGCATTTAAATACCAAAGCATTAAATGATTATGCAGCTTCACTTGTTGAATTG
ATTCCACTTATCAATGAGCATACTGAATTTGGCGATCGTTCCTTAGGTAACAACATCTTA
GTCTATATTTCAAGCTGTCTTGCAGGACGTGGATATCCATCTGGTAAAATTCCTGAAGGT
ATGGTTTCAAATGTTAAACATGAGATTATGAGAATTTTGACAGCTGTACATTCGATGAAT
GCTTCTGATAATGAGCCAACTTATCCTTTTTTGAGAGAACTTTTGAAGTTTGACACCCGC
GAGACTCTGAATGTATTATCATTGGCATTTATGGAGAAAGAATTTAGTACTGAATTGGGA
CTATCACAGCGTCAACGAATAATAAATATATTACTAGAAATTATCAATACTGAAGAGGAT
GATGATAATTCAATGAAGTTTGGTATATTATGCAACTTTATGTCACAACAAATCACTACA
CAAAATCTTCCTGATTCTGCCAGTTTTTTAACACAAATAATTAATTACATCACTTCTGAC
GATCATATCCCAATAAATTCTAGACAACATATTGAAAAAGAGCAAACATTTTTAAATTTA
TTAGAAGCGAATGCACTTTGTGGCAGATTCACGTTTGAGGAAATGCTTGAGATTGCTATG
CGAACAAAATGTTACACAGTTGCACGATTTATATTAGAAAAATTGAAAAGATACGAAAAG
ATAATCGAATGCTTTGTACTGAGTAACAATAGTTATGAATTATTTCGTTATATAATGGAA
TATAAAAATGTAGATGAAAGAAAGATATATCAGCAAGTTCTTGAACATTTTCAATCTATT
CTCGAAATGAATTGTGAAAAGATTTCAAAGTTTGTTATTGAATATTATCCAATTTGTATA
TCACAATTCTTACAGAAAGTTATGAGCATACCTAAACTTCATTATCTATTTCTTCAAGCT
TTAATTTCGAATGGAACAATCAGTTTAGACATTAGTGAACATGACAAATATCTTTCACTT
ATGGCAAACTACAATCCTGAAAATATTTTAGAATTTTTGCAAAATCAAAATCATTCATAT
GATGTTGAAAAAGCATTGACATTATGCGAAGAAAAGAATTTATCAAATGCCATGATTTAT
TTATATGAAAAGAAAGGCGATCACAAGAGAGCTTTCAGTTTAGCAATGGATCTACTTAAA
GAATCGCCAGAAAGTGTTGCTGAATCACAAGCTTTAAAAGTTTGTTCCTTATGTGTACGA
ATTTCAAATGGATTAAATGATGCAGAACGTGAAAGCTATTGGTTTGAACTCATTGAAGCA
GTGTTGTCGAGAAATAATTTGAGTTCAATTGTAAAGCAAGTTTTACATTTATCAAGCAGC
TATGTTGATTTAACTAAACTTGTGCAGTTAATTATGAGAAATGATAATCAAGGATCGGCT
AAAAATTTTGGAGACATAAAGCATATTCTTATTGGAATGTTGACAAATTTCGAATATGAA
TCATTGTTACTAAAAACAACTCAAAATATTCTTGGTAAGGATTTGCATAACAAATTGCTA
AAAGAGAAGCAATCAGCTGAAGCTGGAATTTATTGCAAATTTCTCAAATGTTTTTTGTGC
AAACGTAAGCTCTCAGATTTAGTCATAAGTAATAGCAACAGCAGTAAAACTGACACAAAT
GAAACAGATCAAATTATTATATTTAGTATTTGTGGACATTCCATTCATCAGTCTTGTCTT
GAAAAATCGTTAAAAAATAAGAATGATGACAAATTAAATGAAAAAGATGATGAGATTTAT
GATAAGAATTTAAATTCAATTAAATGCAATGCATGTGGCGTTATAATAAGAGAAGTTGAT
TCAATTTATTTAAACAAAACTAATTGCAAATTGATATCAAATGATAAAAGTGATGTAATG
GAGTTAAAGCTAAAAGCTCCTGCTCGTGTGGGCCTGAGTATTCAAAATTGA

>g13538.t1 Gene=g13538 Length=1276
MDSLKAPSLSSLISGTDRGSSDSLLGSINLDLDDIDDDLSLPPTGELPSLDTVMNEIDSD
VDIDSINNLVPDNRKFSQTPTSSFQEEKQQHQTGSILRHLIFQGVTSQIGSAADRIEAGF
ASAMCVSRMIAIGTSHGFILAFDAAQTLKWCCQEGQKKQQGAVSSLSFNLDDTRLLAGFS
RGAILMINTLTGDVLRILTESISPNAGVLTIKWTSRPTLALSLDSGGSVWSLSFTRRMGI
RGCDSRCLFSGARGEVCTFEPLIVNDESHPFQNNYTLVALATLSKFFILMIRPRLKVIKY
HMLNGPPDSLPLLSWQMVLIQSADTSRSVDPVLATGRANSLYFHQVTYHNGRINVTFLRH
ITLGYNLLSLHWLGPKNIACIERNTEILHLIDVRTSRELESIDVSNFGIIYSSAQFKGIA
TGGNVSKALALAGTFACYSTIVSNDYNSTLYILGKRSLHGINARSWSDRLTYLTNKKQWN
EAFDLAIDAYKSTTEKPRRHVITKERILQLFDDYLNGTTRSPELCLESAIRCLIEIDRTD
LLWQELWDRLYSQETYLNLITQHILNDDLSLISPTISQALLDYWSKVSIEKLEAIILKLE
WQCLDLHQALNFVKNFQLYKALMHLNTKALNDYAASLVELIPLINEHTEFGDRSLGNNIL
VYISSCLAGRGYPSGKIPEGMVSNVKHEIMRILTAVHSMNASDNEPTYPFLRELLKFDTR
ETLNVLSLAFMEKEFSTELGLSQRQRIINILLEIINTEEDDDNSMKFGILCNFMSQQITT
QNLPDSASFLTQIINYITSDDHIPINSRQHIEKEQTFLNLLEANALCGRFTFEEMLEIAM
RTKCYTVARFILEKLKRYEKIIECFVLSNNSYELFRYIMEYKNVDERKIYQQVLEHFQSI
LEMNCEKISKFVIEYYPICISQFLQKVMSIPKLHYLFLQALISNGTISLDISEHDKYLSL
MANYNPENILEFLQNQNHSYDVEKALTLCEEKNLSNAMIYLYEKKGDHKRAFSLAMDLLK
ESPESVAESQALKVCSLCVRISNGLNDAERESYWFELIEAVLSRNNLSSIVKQVLHLSSS
YVDLTKLVQLIMRNDNQGSAKNFGDIKHILIGMLTNFEYESLLLKTTQNILGKDLHNKLL
KEKQSAEAGIYCKFLKCFLCKRKLSDLVISNSNSSKTDTNETDQIIIFSICGHSIHQSCL
EKSLKNKNDDKLNEKDDEIYDKNLNSIKCNACGVIIREVDSIYLNKTNCKLISNDKSDVM
ELKLKAPARVGLSIQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13538.t1 Gene3D G3DSA:2.130.10.10 - 92 275 0.0000027
9 g13538.t1 Gene3D G3DSA:1.25.40.10 - 825 1223 0.0000000
3 g13538.t1 PANTHER PTHR12616 VACUOLAR PROTEIN SORTING VPS41 79 1216 0.0000000
4 g13538.t1 PANTHER PTHR12616:SF8 VPS8 SUBUNIT OF CORVET COMPLEX 79 1216 0.0000000
2 g13538.t1 Pfam PF12816 Golgi CORVET complex core vacuolar protein 8 556 730 0.0000000
1 g13538.t1 Pfam PF00637 Region in Clathrin and VPS 935 1020 0.0000000
10 g13538.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 887 1070 13.9540000
7 g13538.t1 SUPERFAMILY SSF50998 Quinoprotein alcohol dehydrogenase-like 123 414 0.0000000
5 g13538.t1 SUPERFAMILY SSF48371 ARM repeat 837 1074 0.0000005
6 g13538.t1 SUPERFAMILY SSF57850 RING/U-box 1156 1210 0.0000600

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
GO:0005515 protein binding 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