Gene loci information

Transcript annotation

  • This transcript has been annotated as Vacuolar protein sorting-associated protein 11-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_2 g8967 g8967.t1 TSS g8967.t1 34256367 34256367
chr_2 g8967 g8967.t1 isoform g8967.t1 34256523 34259937
chr_2 g8967 g8967.t1 exon g8967.t1.exon1 34256523 34256531
chr_2 g8967 g8967.t1 cds g8967.t1.CDS1 34256523 34256531
chr_2 g8967 g8967.t1 exon g8967.t1.exon2 34256602 34256670
chr_2 g8967 g8967.t1 cds g8967.t1.CDS2 34256602 34256670
chr_2 g8967 g8967.t1 exon g8967.t1.exon3 34256728 34256901
chr_2 g8967 g8967.t1 cds g8967.t1.CDS3 34256728 34256901
chr_2 g8967 g8967.t1 exon g8967.t1.exon4 34256966 34259801
chr_2 g8967 g8967.t1 cds g8967.t1.CDS4 34256966 34259801
chr_2 g8967 g8967.t1 exon g8967.t1.exon5 34259861 34259937
chr_2 g8967 g8967.t1 cds g8967.t1.CDS5 34259861 34259937
chr_2 g8967 g8967.t1 TTS g8967.t1 NA NA

Sequences

>g8967.t1 Gene=g8967 Length=3165
ATGCTTGAATGGAGGAAATTTGATTTCTTTGATTTAAAACCAATTGTCGATGAAGATGCA
TTTTCAAGCGTTCTTTCAGAATCTGATTTCGTAACTTCAACTTCAGGAAATAATCAAATA
ATTATAGGCGATTCAAAAGGTTTTGTTCATGTATTTCCAAAGAATTTTCGTGATTCCTAC
ACTTTTAAGGCTCATAATTGTATTACACATTGTGAACTTTCATTCCAAAATAATTTACTC
GTCACACTCGGTAATGATGAATTCACAGATTCATTGCCTGAATTCAAAGTTTGGAATCTG
AATAAACTTATTAAATCAATACCGGCATGTGTTCGTACAGTGAAAACTAATTTACAAAGA
GCAACAGCACTTGGAGTGTCTGAAAATGGACAACATATGGCAATCGGATTCGAGAGAGGC
AATATAACGGTTTATAAGGGTGATATTGCTCGTGATAAAACAAAGTCAGTAAAAAATATT
ACATTTGGTACTGCTTCTATTAAGGGAATAGAATTTAAACAAGTTGGCAAAATTACGCAT
ATGTTTGTGTGCTCAGATTCGGGCGTTTATTTATATACTATGCATAGTCGTGATAAAGAA
TTGAAAAATGTTTTAGATACAAGCAGTGCAAACATGGTAATGACTTGTAAATGGCTACAA
ACAGCAGCAAATTCAGAGGGTTATTTTATGGTCGGCAGAGATGATGCAATTTATTGTTAT
ACGACAGAAGGTCGAGCTCCATGTTATGCTTTTGACGGAAGAAAAGTGCTCATTAGATGG
TTTCGAAATCATTTATTAATGGTCACTTGTCCAATCATGGAAAATCCTCTTCAAACAAAA
CCTCACACTTTAACCGTAATTGATGTCATAAATCGATTCATAGTTTTTACTACACAAGTT
GAAACAGTATCATCCGTTTTTGTTGAATATGGAACATGTTATGTTCTCACAAAAAATAAA
TTAATGTATCATCTTGATGAAAAAGATTTACAAAGTAAATTAAACTCACTTTATAAAAAG
AATATGTACGATACTGCTGTTAAAATAGCTAAAAACAATCAATATGATGCCGAAGGATTA
TCAAATATTTTCAAACAATATGGTGATCATTTATATAATAAAGGAAATTTTGCAAGTGCT
GTTGAACAATATATCAAAACAATTGGTTATCTTGAGCCATCATATGTAATTAGGCGTTTC
TTAGATTCAAGACATACACAATTTTTGACTGATTATTTACAACATATTCACAAAGAAGGA
AAAGCATCAACTGATCATACAACATTATTACTAAATTGTTTCACTCGTCTCGATCGTATT
GATGAGTTGAAGACATTTTTAGAAAATTACAAACAAAATCATTTTGATATTGATGTAGCA
ATCAATGTTTGTCGCAAATCTTGTATTGAACAAGCTCTTGATTTAGCAAAGTTTAATAAT
AAATATGATCATGCTATCTCAATTATGATTGAAGATTTAAAACATTATGATAATGCAGTT
GAATATTTATCAAAGCTCTCTTATGACGATGCTGAAAGAAATATTATGAAATATGGAAAT
TTGTTAATGGATTATGTGCCACATAAATTGATTACGTTGCTCAAAAAGTTATGCACAGAT
TATATTGCAAAAAAGTGTGATGAGTCATCTAGAAAAGATCACAGTGAGGATAATGACATT
TTTACGCTCGGTTATCGTAATGGTGGATTTTTAGATGAGCGTGAACAAGCAACACCTGAA
GATTTTATTCATTTATTCAATGACTCGAAGCAAATGATTGACTATATAGAATACTTGATT
AGAAATTTGCCAACGTGTTCAAATTTTCTCTACAATTCTCTTATTGAGCATTATCTTACA
TTATGGAAAATGTCTGATAATCCTTCAAGTGAACGAACGGGACTTGAGCAACGTTTAGTT
GAGCTTATTAAAAATTTCAATCAATTCTATGATGATAATCATGTTTTAGTGTTGTGCAAG
ACTTATGAATTTTGGCTTGGTGCAATGTTAATTTACGAAGAAAAGAAGCTTTATAATTTA
ATTGTCCGTCATTATTTAAATACAAAAGATTTTGGCAGTTTATATGGTTTATGCAAAAGA
TTAGGTCCAACAGATTCTTCAATTTGGCTTGCTACTCTTAATGGGCTAAAATCAAGTAAT
CAAGTTCCATCTTCATTTCTTCAAGAGATACTTCAAGTTATTGCAACAGAAAAGCTTCAG
TCACCACTTCAAGTGCTCAATATTTTAACATCTATCGATAATGGACCAAATTTGTCAACC
GTTCGCAGTTATTTCATGTCATCGTTTCAAAAGGAAGATGAAATCATTAAAAAGGATAGA
GAGGCAGCAGAAAAATATCACAATGAAACAGAAGAGCTAAAAAATAATATTGAAACAATG
AATAGAAAGCCAATCGAATTTCGTGGTAGTTTATGCGATGCATGTCATCAACCGCTCAAC
TTTCCGTCTCTTTTCTTTCTCTGTAAGCATTCATTTCATCAGGATTGCATAAGAAGCTTC
TCAGAAACTGAAAAAGATTGCATGGTTTGTAGAAAGAAAAATACACAATTGCTTGATACG
ATGCATATTCAGAATGAAAGTCGTAATAAAAATCACATTTTTCAAGAGGAAATTGAAAAA
TCTCATGAACCTTTTGGTGTAGTTGCTGAATATTTTTCGCGTAGTCTTTTCAATAAAATT
GTTTTACTTTCTGATGACGATGATGAGAATAGAGAAAAGTTTGATGACATTAAATTATCA
AGAAAACCACAACAGAAACAATATGAGACAAAACCACTGCCAAATACTTCAGAAGGAAAA
ATTCGCTTAGAAGAGACATTAGGAACAAATGTTCAACACAAACCACAATTGTCAGAGGGT
AGATTAAGATTACAAGAACAAAGTTATAATAAGAGTAAGCCTATTGAACGTTTTGCTACT
CAATCGAAACCACAACAACAGCAATCAATTCGTAAAAAGCAAGAAGTTAAAGTAAACTAT
CCAATATCTTCTAATCCGTTTGATGACGATGATGATGATATTAAAAATGAAAATTATAAT
GAAGCATTAAATCCATTTGCTGATGAAGATGAAGTAATTGATGCAGTTGAAAGTGTTAAA
ACTCCAATATCTACAAATCCTTTTGGTGATGAAGACGATGAATAA

>g8967.t1 Gene=g8967 Length=1054
MLEWRKFDFFDLKPIVDEDAFSSVLSESDFVTSTSGNNQIIIGDSKGFVHVFPKNFRDSY
TFKAHNCITHCELSFQNNLLVTLGNDEFTDSLPEFKVWNLNKLIKSIPACVRTVKTNLQR
ATALGVSENGQHMAIGFERGNITVYKGDIARDKTKSVKNITFGTASIKGIEFKQVGKITH
MFVCSDSGVYLYTMHSRDKELKNVLDTSSANMVMTCKWLQTAANSEGYFMVGRDDAIYCY
TTEGRAPCYAFDGRKVLIRWFRNHLLMVTCPIMENPLQTKPHTLTVIDVINRFIVFTTQV
ETVSSVFVEYGTCYVLTKNKLMYHLDEKDLQSKLNSLYKKNMYDTAVKIAKNNQYDAEGL
SNIFKQYGDHLYNKGNFASAVEQYIKTIGYLEPSYVIRRFLDSRHTQFLTDYLQHIHKEG
KASTDHTTLLLNCFTRLDRIDELKTFLENYKQNHFDIDVAINVCRKSCIEQALDLAKFNN
KYDHAISIMIEDLKHYDNAVEYLSKLSYDDAERNIMKYGNLLMDYVPHKLITLLKKLCTD
YIAKKCDESSRKDHSEDNDIFTLGYRNGGFLDEREQATPEDFIHLFNDSKQMIDYIEYLI
RNLPTCSNFLYNSLIEHYLTLWKMSDNPSSERTGLEQRLVELIKNFNQFYDDNHVLVLCK
TYEFWLGAMLIYEEKKLYNLIVRHYLNTKDFGSLYGLCKRLGPTDSSIWLATLNGLKSSN
QVPSSFLQEILQVIATEKLQSPLQVLNILTSIDNGPNLSTVRSYFMSSFQKEDEIIKKDR
EAAEKYHNETEELKNNIETMNRKPIEFRGSLCDACHQPLNFPSLFFLCKHSFHQDCIRSF
SETEKDCMVCRKKNTQLLDTMHIQNESRNKNHIFQEEIEKSHEPFGVVAEYFSRSLFNKI
VLLSDDDDENREKFDDIKLSRKPQQKQYETKPLPNTSEGKIRLEETLGTNVQHKPQLSEG
RLRLQEQSYNKSKPIERFATQSKPQQQQSIRKKQEVKVNYPISSNPFDDDDDDIKNENYN
EALNPFADEDEVIDAVESVKTPISTNPFGDEDDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8967.t1 CDD cd16688 RING-H2_Vps11 812 851 8.1142E-14
11 g8967.t1 Coils Coil Coil 776 803 -
9 g8967.t1 Gene3D G3DSA:2.130.10.10 - 18 272 1.3E-10
10 g8967.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 789 882 1.4E-7
15 g8967.t1 MobiDBLite mobidb-lite consensus disorder prediction 914 960 -
14 g8967.t1 MobiDBLite mobidb-lite consensus disorder prediction 975 1001 -
16 g8967.t1 MobiDBLite mobidb-lite consensus disorder prediction 975 1012 -
3 g8967.t1 PANTHER PTHR23323:SF24 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 11 HOMOLOG 3 898 2.3E-231
4 g8967.t1 PANTHER PTHR23323 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 3 898 2.3E-231
12 g8967.t1 PIRSF PIRSF007860 Vps11 1 903 1.1E-197
2 g8967.t1 Pfam PF00637 Region in Clathrin and VPS 392 509 2.9E-12
1 g8967.t1 Pfam PF12451 Vacuolar protein sorting protein 11 C terminal 857 898 2.4E-6
20 g8967.t1 ProSiteProfiles PS50168 Death effector domain (DED) profile. 366 448 9.564
19 g8967.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 384 531 24.143
18 g8967.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 570 725 10.144
17 g8967.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 812 851 9.908
8 g8967.t1 SUPERFAMILY SSF50978 WD40 repeat-like 33 251 2.85E-13
5 g8967.t1 SUPERFAMILY SSF48371 ARM repeat 335 621 3.17E-5
6 g8967.t1 SUPERFAMILY SSF48371 ARM repeat 590 801 2.65E-5
7 g8967.t1 SUPERFAMILY SSF57850 RING/U-box 811 859 1.1E-7

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:0042981 regulation of apoptotic process BP
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