Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vesicle transport protein SEC20.

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 g1593 g1593.t4 TTS g1593.t4 12050956 12050956
chr_3 g1593 g1593.t4 isoform g1593.t4 12050962 12052230
chr_3 g1593 g1593.t4 exon g1593.t4.exon1 12050962 12051847
chr_3 g1593 g1593.t4 cds g1593.t4.CDS1 12051276 12051847
chr_3 g1593 g1593.t4 exon g1593.t4.exon2 12052158 12052230
chr_3 g1593 g1593.t4 cds g1593.t4.CDS2 12052158 12052230
chr_3 g1593 g1593.t4 TSS g1593.t4 12052321 12052321

Sequences

>g1593.t4 Gene=g1593 Length=959
ATGGAATCACAACGGCTACTAAAGCAAGAGATAATTGATCATAACTTACAAGTTAAAGCC
ATCATCCAGGCAACATTTCGTGGATCATTACAAGACCTAGAATTGTTAAATGAAGCAGGT
AGAGCAAAACTTGCACAATTAAGGAAATGTATTGAGAAATTAGATGATTGGGCGAGAGAT
GAAAATGATCCACAGCTCTCAAATGATGTCGACTCACATCGTGAACAATTTTCAAAAACT
TTGCAGGCATTTAGGAAAGCGAATATTAGCACAATGTTAGAAATAGAAAAGAGTGATAAG
GCGGAATTGTTTACAATTAAACCTGAAGCAGAACTTCGGCATAGAACTGCTAGTAATCTA
ATATCACAACAAGAGAGTGTGACAGAACGTATGCTTAGTATATCAAGAAATTTGGCTGAA
ACTACACAAAAATCAGCAGCAACTCTTGATTCACTTATTCAATCTTCATCAACTGTCGAT
GGCACAAATGATGAATTATCGAACACAGCTGGTACAATTCAACAGTCAGGAAAATTACTC
AACAAATATGGACGAAGGGAAACTACTGATAAAATTTTACTCTTCCTTGCATTCTTCTTC
TTTCTCGCTGTTGTGTTTTATATTGTGCAAAAGAGAATGTTTTAAAAATGTTGACTCTAT
AATTATAATATTTTATTTTTGTACTTTAATTGATTTTGAAAATGAAAAGCTTGTGAGAAA
TTGACTTTGAGAGCGAGACTTGTATGTAAATAATTTATCGGAAATTACAAGATAAAGACA
CTTTAATTTGTACCAAAAAAGAAATCAAAGTGTCATGATCTTTAAAATATGTAAATTTTC
TAAACTAAATGCATTTTATGAAAAGAAAAAAATTTATTATATTATAAAATTATTCTGCTC
AATTCCCAACACTTAAGACAAAGTCTTAATAAAATGAAACCTTAAAATTATATTGAATT

>g1593.t4 Gene=g1593 Length=214
MESQRLLKQEIIDHNLQVKAIIQATFRGSLQDLELLNEAGRAKLAQLRKCIEKLDDWARD
ENDPQLSNDVDSHREQFSKTLQAFRKANISTMLEIEKSDKAELFTIKPEAELRHRTASNL
ISQQESVTERMLSISRNLAETTQKSAATLDSLIQSSSTVDGTNDELSNTAGTIQQSGKLL
NKYGRRETTDKILLFLAFFFFLAVVFYIVQKRMF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g1593.t4 PANTHER PTHR12825:SF0 VESICLE TRANSPORT PROTEIN SEC20 5 214 9.2E-37
3 g1593.t4 PANTHER PTHR12825 BNIP1-RELATED 5 214 9.2E-37
1 g1593.t4 Pfam PF03908 Sec20 122 213 3.9E-27
5 g1593.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 191 -
7 g1593.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 192 209 -
6 g1593.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 210 214 -
4 g1593.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 192 209 -

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:0005484 SNAP receptor activity MF
GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum 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. There were no conditions that were differentially expressed