Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Syntaxin-1A.

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 g959 g959.t12 TSS g959.t12 7041748 7041748
chr_3 g959 g959.t12 isoform g959.t12 7042263 7060460
chr_3 g959 g959.t12 exon g959.t12.exon1 7042263 7042295
chr_3 g959 g959.t12 exon g959.t12.exon2 7051815 7051995
chr_3 g959 g959.t12 exon g959.t12.exon3 7052074 7052128
chr_3 g959 g959.t12 exon g959.t12.exon4 7052331 7052530
chr_3 g959 g959.t12 exon g959.t12.exon5 7052601 7052678
chr_3 g959 g959.t12 cds g959.t12.CDS1 7052619 7052678
chr_3 g959 g959.t12 exon g959.t12.exon6 7052753 7052890
chr_3 g959 g959.t12 cds g959.t12.CDS2 7052753 7052890
chr_3 g959 g959.t12 exon g959.t12.exon7 7054214 7054324
chr_3 g959 g959.t12 cds g959.t12.CDS3 7054214 7054324
chr_3 g959 g959.t12 exon g959.t12.exon8 7060239 7060460
chr_3 g959 g959.t12 cds g959.t12.CDS4 7060239 7060316
chr_3 g959 g959.t12 TTS g959.t12 7060535 7060535

Sequences

>g959.t12 Gene=g959 Length=1018
ATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGACGAGGATGCGGGG
ATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTTCACTGAGGTGGAA
GAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGTTAAGAAAAAACAC
AGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGCAAGAGTTAGAGGATCTG
ATGGCAGATATTAAGAAAAATGCCAATAGATACAAATAAATATAGAATATCGAACAAAGT
ATCGAGCAAGAAGAGCAGAGTAAATCAGCAAGTGCCGATTTACGAATACGTAAGACACAA
CATTCGACATTATCACGAAAATTTGTCGAAGTAATGACAGAATATAATCGAACACAAACT
GATTATCGAGAGAGATGTAAAGCGAGAATACAACGTCAATTGGAAATCACTGGTAAAGCC
ACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCGGCAGTGTTTACACAA
GGAGTATATTATTATGGAAACACAACAAGCAAAACAGACCCTGGCAGATATCGAAGCACG
ACATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGCACGATATGTTCATGGA
TATGGCAATGTTGGTCGAGAGTCAGGGAGAATTGGTGGATCGGATTGAGAACCATGTTGA
GGAGGGCAAGGATTTCACTGAAAATGCAAAGAAGCAAATTTATCAGGCTTCCGTGTATGC
GAAAAAGGCGAGGAAGAAAAAAATTTATATCATAATCTGCCTGACGATAGTAGGAATTCT
ATTGCTATTGTATCTATACAGTCTCATCTTTTGATTGGAATAACTGCCACTTCAGCAAAA
AACACAACGACTATTTATGATGTCATCTATCTAATCTATATAATTTTTTGTTCTACAAGT
TGTCATTATACTTTTATATGTATATTTGTCATCGAAGTATCCTTTTTATTGCATTGTT

>g959.t12 Gene=g959 Length=128
MKNSKKCWSKEIRQCLHKEYIIMETQQAKQTLADIEARHADIIKLENSIRELHDMFMDMA
MLVESQGELVDRIENHVEEGKDFTENAKKQIYQASVYAKKARKKKIYIIICLTIVGILLL
LYLYSLIF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g959.t12 Gene3D G3DSA:1.20.5.110 - 21 127 2.5E-38
3 g959.t12 PANTHER PTHR19957:SF231 SYNTAXIN-1A HOMOLOG 19 122 2.4E-37
4 g959.t12 PANTHER PTHR19957 SYNTAXIN 19 122 2.4E-37
1 g959.t12 Pfam PF00804 Syntaxin 20 67 7.5E-17
2 g959.t12 Pfam PF05739 SNARE domain 68 120 9.8E-15
7 g959.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 105 -
9 g959.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 106 127 -
8 g959.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 128 128 -
11 g959.t12 ProSitePatterns PS00914 Syntaxin / epimorphin family signature. 38 77 -
13 g959.t12 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 32 94 18.321
12 g959.t12 SMART SM00397 tSNARE_6 27 94 7.2E-19
5 g959.t12 SUPERFAMILY SSF47661 t-snare proteins 19 87 1.49E-24
10 g959.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 106 127 -

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:0016020 membrane CC
GO:0006886 intracellular protein transport BP
GO:0005484 SNAP receptor activity 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