Gene loci information

Transcript annotation

  • This transcript has been annotated as Vam6/Vps39-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_3 g3897 g3897.t1 isoform g3897.t1 28698858 28701752
chr_3 g3897 g3897.t1 exon g3897.t1.exon1 28698858 28699160
chr_3 g3897 g3897.t1 cds g3897.t1.CDS1 28698858 28699160
chr_3 g3897 g3897.t1 exon g3897.t1.exon2 28699213 28701251
chr_3 g3897 g3897.t1 cds g3897.t1.CDS2 28699213 28701251
chr_3 g3897 g3897.t1 exon g3897.t1.exon3 28701318 28701586
chr_3 g3897 g3897.t1 cds g3897.t1.CDS3 28701318 28701586
chr_3 g3897 g3897.t1 exon g3897.t1.exon4 28701658 28701752
chr_3 g3897 g3897.t1 cds g3897.t1.CDS4 28701658 28701752
chr_3 g3897 g3897.t1 TSS g3897.t1 28701838 28701838
chr_3 g3897 g3897.t1 TTS g3897.t1 NA NA

Sequences

>g3897.t1 Gene=g3897 Length=2706
ATGCATAAAGCATACACATTACATCCGCCATCAAAAATATCTGTTCAAATTGAATCAATA
GCAGGCTATAAGAACAATGTAATTCTAGGAACAAGGCAAGGCCATTTGCTTCAATATTGT
TTTCAAGAATCAGCAGATGGTAAAATGGAATTACAATTGCTTCAATATGACAAGAATTTC
AGCAAAAAACCGATTTTGCAATTGCAAGTTATTGAAGATCTGAATCTTTTGTTTAGTCTC
TCTGATAACATCATATCGATTAATGATATTTCTCGCCATAATTTTCCTCTTATTCATCTT
GCTACTAAGACTAAAGGAGCAAATACATTTTCAATGGACATTCAAAAGACTCAAAGTTTA
ACAGATCAAGTAAGTTTAGTTGTGAGATTATGTGTTGCAGTAAAAAGGAAACTTCAGTTT
TATTATTGGAAGAGAAATGAATTGCTTGAATTTGCAGCAGATATTGAGCTTTCAGATGTA
CCTAAAGTTGTTGCTTGGACAGGAAATCAAATTTGTATTGGTTATAAAACAGAATATATT
CTCTATGATATATCAGACGATAAGAGAAAGAAACACGATCTCTTTCCAACGACAAGCTCT
TCTAGATCAATTGATCCTTGTGTCTCCCTTATTGATAGCGAAAAATTTTTCGCTGTTGTG
AAAGACGAACATTTAATTACAATACCTACATCCGATGAAGCAAAAAATAATTCATTAAAA
TTGGATAGCAAAGCTTCAATTTTAGATCCAAAAAGTAATAAAGCCTATCCCACAATTACA
TGGTCCGAACCTCCGCTTTTAGTTGTATGGGATCCGCCATATTTATTAGGCTTACTAACA
GATATAGTTGAAGTGCGTGTGCTTGACACTTCTGGTTTAGAAAAGGATAATCTTATTCAG
ACTATTCCAGAATTACAAAAAGCAAGATTTCTTATAAATGGACGAAATAATCAACAAGGT
TTGATTTTTGCTGCATCTACATCTCATTTATGGTGCATTGAAAGCATAGACATTGCAACA
CAAAGACAACATTTATTACAAGACAAGAAATGGTTTCTTGCACTTCAACTAACATCAATG
TCTGACGAATCAGAAGAAGATAAGCAATCAATGACACATGAAATTCAAACACTTTACGCT
TATGATTTATTCATCAATAAACAATTTCGCGAAGCAATGCTTGAATTTTCCAAACTTAAA
ACTGATCCAACAAATGTCATCAAATTGTTTCCAGACTTACTGCCGTCATGTGAACCAGTA
CCAGCAAATCTATCGAGATCAATGTCATCTTCAATGGCCGAAACAGAATTAATGCGTGAA
CTACCAAAACTGGCAGATAAAGATTTGGAAAACGGATTATTAGCGTTAATTGATTACTTA
GTAGAGATACGCTCACAAGTGGGTAAAATACAAGGAAATGCTAAAGCTTTTGGAAGAAAT
CCTAAAGTTTTGCTCTCTATCATTGATACAACACTATTGAAAACTTATTTGGAAACGAAT
GACTCATTTGTAAGTTCTTTAATACGACTTAACAATTGTCATTTAGAAGAATCGGAAAAG
ATTTTGAAATCATATAAAAAATTTGGGGAATTAATTATACTTTATCAAACAAAAGGACAG
CACAGACGTGCATTGACATTGCTTAAAGCTTCATCAAATTTCGGATATGAAAGAACAATT
CAATATCTACAACACTTGGGTGCTGAGCACAAAAAATTAATTTTTGAATTTGCTGACTGG
GTCATTCAAGAACATCCTCAAGATGGATTAAAAATTTTTACTGAAGACATACAAGAAGTT
GAAAATTTACCACGAGCTGATGTGCTAGATTTTCTCTTGAAAAGTCACAAAAATCTTGTC
GTTCCCTATTTGGAACACATAATTAATGTGTGGGATGAAGTTAAACCATTATTTCATAAT
ATTTTAATTCAACAGTATAAAGAACAAATATTTAATTTGCAAACTGATCCTGATCTCGAA
AAAGTTTACCAAAAAAAGCTGGAACTTCAAGAAATTCGTGAGAAATTGGTCAATTTTCTT
AAAACTTCTAATAATTATGCTGCAGAAAAAGTTCTCGTTGAATTTCCTTTCAATGATTTA
TTTGAAGAACGCGCTATTGTATTGGGAAAATTAAACAAGCATGAAAAAGTTTTAGCCATA
TACATTCAAATCCTTGGTGATGTAGAAAAAGCAATTGAGTATTGTGATCAAGTTTTCATG
TCCGCTAGTGTCAATCATAATGATGTGTACATAATTTTAATTCGATTGCTTCTTAATCCA
CCGACTGTTCCACCATATAACGAAGTAAAATTACACGAGAAATGCTTACAACCAGACATT
GAAGCTGTTCTTGATATACTTGAGAAAAATGCGAAAAAAATCAATCCACATTCCGTTTTA
ACTATTTTACCTGATAACATTCCAATTAAAAGACTCAAAAGATTTTTAGAAGTAGCACTT
CACAGTCAACTTGAACAAAAGAGAAAATTACAAATTCTAAAAGGACTCTACTATGCTGAA
AATTTACAGTGTAAAGAGCAAAACATGATTTGTGAATCAAGAAGTTTCTTAATCACGGAA
CTTACATTATGTGCGGTGTGTAAAAGAAAATTTAGTAATCAGTCTGCTTTTGTGCGTTTA
GCAAATGGCGATTTAATTCATATAAATTGTCAAAATAAGGAGTTTGATGCTACTAAAATT
ATTTAA

>g3897.t1 Gene=g3897 Length=901
MHKAYTLHPPSKISVQIESIAGYKNNVILGTRQGHLLQYCFQESADGKMELQLLQYDKNF
SKKPILQLQVIEDLNLLFSLSDNIISINDISRHNFPLIHLATKTKGANTFSMDIQKTQSL
TDQVSLVVRLCVAVKRKLQFYYWKRNELLEFAADIELSDVPKVVAWTGNQICIGYKTEYI
LYDISDDKRKKHDLFPTTSSSRSIDPCVSLIDSEKFFAVVKDEHLITIPTSDEAKNNSLK
LDSKASILDPKSNKAYPTITWSEPPLLVVWDPPYLLGLLTDIVEVRVLDTSGLEKDNLIQ
TIPELQKARFLINGRNNQQGLIFAASTSHLWCIESIDIATQRQHLLQDKKWFLALQLTSM
SDESEEDKQSMTHEIQTLYAYDLFINKQFREAMLEFSKLKTDPTNVIKLFPDLLPSCEPV
PANLSRSMSSSMAETELMRELPKLADKDLENGLLALIDYLVEIRSQVGKIQGNAKAFGRN
PKVLLSIIDTTLLKTYLETNDSFVSSLIRLNNCHLEESEKILKSYKKFGELIILYQTKGQ
HRRALTLLKASSNFGYERTIQYLQHLGAEHKKLIFEFADWVIQEHPQDGLKIFTEDIQEV
ENLPRADVLDFLLKSHKNLVVPYLEHIINVWDEVKPLFHNILIQQYKEQIFNLQTDPDLE
KVYQKKLELQEIREKLVNFLKTSNNYAAEKVLVEFPFNDLFEERAIVLGKLNKHEKVLAI
YIQILGDVEKAIEYCDQVFMSASVNHNDVYIILIRLLLNPPTVPPYNEVKLHEKCLQPDI
EAVLDILEKNAKKINPHSVLTILPDNIPIKRLKRFLEVALHSQLEQKRKLQILKGLYYAE
NLQCKEQNMICESRSFLITELTLCAVCKRKFSNQSAFVRLANGDLIHINCQNKEFDATKI
I

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g3897.t1 PANTHER PTHR12894 CNH DOMAIN CONTAINING 7 893 0.000
2 g3897.t1 Pfam PF00780 CNH domain 58 314 0.000
3 g3897.t1 Pfam PF10366 Vacuolar sorting protein 39 domain 1 488 582 0.000
1 g3897.t1 Pfam PF10367 Vacuolar sorting protein 39 domain 2 784 892 0.000
6 g3897.t1 ProSiteProfiles PS50219 Citron homology (CNH) domain profile. 14 318 24.153
5 g3897.t1 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 596 762 20.900

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:0016192 vesicle-mediated transport BP

KEGG

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