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.t5 isoform g13494.t5 30510723 30511809
chr_1 g13494 g13494.t5 exon g13494.t5.exon1 30510723 30511473
chr_1 g13494 g13494.t5 cds g13494.t5.CDS1 30510796 30511473
chr_1 g13494 g13494.t5 exon g13494.t5.exon2 30511537 30511809
chr_1 g13494 g13494.t5 cds g13494.t5.CDS2 30511537 30511809
chr_1 g13494 g13494.t5 TTS g13494.t5 30511979 30511979
chr_1 g13494 g13494.t5 TSS g13494.t5 NA NA

Sequences

>g13494.t5 Gene=g13494 Length=1024
AGAAAAGAAAATTTTACTTGAAGCTCTTGCAATTCTTTATTCACATGAGCGAGAATATGA
CAAAGCAGTGACAATGTACATTAAATTAGAACACAAAGATGTCTTTCAATTAATTAAAAA
TCATAAACTGTACAACGTTATTAAACCAATGATTGTTGATCTGATGAAATTAGATACTGA
AAAAGCCATCAATATTCTCCTCAGTCAAAATGATATTTCACCAGCTGAAATTGTTGAAAA
GTTAAAGAAAAGTGAGAATGAAATGTTCCTGTATCAGTATTTGGATGCCTTTAAGAGAAT
TGATAGAGCAGGAAAATTTGATTGGGAATTACTTAATCTTTATACGAAATATGATCGAGA
TAAGATGCTACCATTGCTCAAAAGATCGTATGAATATCCTCTGCAAGATGCTTATGAATT
ATGTAAAGTAAATTTATTCTATCCTGAAATGGTATACTTGTTAGAAAGATTAGGAAACAC
AAATGAAGCATTAGAAATTATTTTAAAGAAAATGGAAAATATTCGAATGGCGATAAACTT
TTGCTGTGAGCATGATGACAGGGAATTATGGGAACATTTAATTAGCGAAAGCTTTGAAAA
ACCTGAAATTATTACTCTACTAATGGATGGAATTTCCGGTTATTCAATCTCTATTGATCC
ACAAATGCTTATTGATCGACTTCATGAAGGACAAGAAATTCCAGAACTTAAAAAAGCTCT
CACAAAAATGCTAACGGGTTATAGCTTACAAGTATCAATACACGAAGGATGCAATCAAAT
TCTCAAAACAGATTATTTTGATGTTCATAATAAACTCATCAAACAACAAGGAAAGGCAAT
GTACTTTGGAAGTCAAACAGTCTGCAGTCTCTGTCAACGAAGCATAGTCAATATAAAGGA
TAGAAATTCCAATAAAACTCCTCCAGATATTATTGTTTTCAATTGCAAACACATTTTCCA
TGAGTCATGTAAATTTGATCATGACTATTGTTCCATATGTATTCCAACAAAAGAAGTCCC
ATAA

>g13494.t5 Gene=g13494 Length=316
MYIKLEHKDVFQLIKNHKLYNVIKPMIVDLMKLDTEKAINILLSQNDISPAEIVEKLKKS
ENEMFLYQYLDAFKRIDRAGKFDWELLNLYTKYDRDKMLPLLKRSYEYPLQDAYELCKVN
LFYPEMVYLLERLGNTNEALEIILKKMENIRMAINFCCEHDDRELWEHLISESFEKPEII
TLLMDGISGYSISIDPQMLIDRLHEGQEIPELKKALTKMLTGYSLQVSIHEGCNQILKTD
YFDVHNKLIKQQGKAMYFGSQTVCSLCQRSIVNIKDRNSNKTPPDIIVFNCKHIFHESCK
FDHDYCSICIPTKEVP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g13494.t5 Coils Coil Coil 130 150 -
5 g13494.t5 Gene3D G3DSA:1.25.40.10 - 29 254 8.8E-23
2 g13494.t5 PANTHER PTHR12616:SF1 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG 1 300 2.9E-72
3 g13494.t5 PANTHER PTHR12616 VACUOLAR PROTEIN SORTING VPS41 1 300 2.9E-72
1 g13494.t5 Pfam PF00637 Region in Clathrin and VPS 44 179 9.2E-18
8 g13494.t5 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 41 182 20.375
7 g13494.t5 ProSiteProfiles PS50089 Zinc finger RING-type profile. 264 309 8.535
4 g13494.t5 SMART SM00299 CLH_2 41 182 1.2E-12

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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