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.t16 isoform g959.t16 7052529 7060460
chr_3 g959 g959.t16 exon g959.t16.exon1 7052529 7052530
chr_3 g959 g959.t16 exon g959.t16.exon2 7052601 7052674
chr_3 g959 g959.t16 cds g959.t16.CDS1 7052636 7052674
chr_3 g959 g959.t16 exon g959.t16.exon3 7052753 7052890
chr_3 g959 g959.t16 cds g959.t16.CDS2 7052753 7052890
chr_3 g959 g959.t16 exon g959.t16.exon4 7054214 7054324
chr_3 g959 g959.t16 cds g959.t16.CDS3 7054214 7054324
chr_3 g959 g959.t16 exon g959.t16.exon5 7060239 7060460
chr_3 g959 g959.t16 cds g959.t16.CDS4 7060239 7060316
chr_3 g959 g959.t16 TTS g959.t16 7060535 7060535
chr_3 g959 g959.t16 TSS g959.t16 NA NA

Sequences

>g959.t16 Gene=g959 Length=547
CACTGGTAAAGCCACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCGGC
AGTGTTTACACAAGGAATTATTATGGAAACACAACAAGCAAAACAGACCCTGGCAGATAT
CGAAGCACGACATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGCACGATAT
GTTCATGGATATGGCAATGTTGGTCGAGAGTCAGGGAGAATTGGTGGATCGGATTGAGAA
CCATGTTGAGGAGGGCAAGGATTTCACTGAAAATGCAAAGAAGCAAATTTATCAGGCTTC
CGTGTATGCGAAAAAGGCGAGGAAGAAAAAAATTTATATCATAATCTGCCTGACGATAGT
AGGAATTCTATTGCTATTGTATCTATACAGTCTCATCTTTTGATTGGAATAACTGCCACT
TCAGCAAAAAACACAACGACTATTTATGATGTCATCTATCTAATCTATATAATTTTTTGT
TCTACAAGTTGTCATTATACTTTTATATGTATATTTGTCATCGAAGTATCCTTTTTATTG
CATTGTT

>g959.t16 Gene=g959 Length=121
MLEQGNSAVFTQGIIMETQQAKQTLADIEARHADIIKLENSIRELHDMFMDMAMLVESQG
ELVDRIENHVEEGKDFTENAKKQIYQASVYAKKARKKKIYIIICLTIVGILLLLYLYSLI
F

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g959.t16 Gene3D G3DSA:1.20.5.110 - 13 120 8.6E-39
3 g959.t16 PANTHER PTHR19957:SF231 SYNTAXIN-1A HOMOLOG 1 115 1.6E-44
4 g959.t16 PANTHER PTHR19957 SYNTAXIN 1 115 1.6E-44
1 g959.t16 Pfam PF00804 Syntaxin 1 60 1.2E-21
2 g959.t16 Pfam PF05739 SNARE domain 61 113 8.6E-15
7 g959.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 98 -
9 g959.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 120 -
8 g959.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 121 121 -
11 g959.t16 ProSitePatterns PS00914 Syntaxin / epimorphin family signature. 31 70 -
13 g959.t16 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 25 87 18.321
12 g959.t16 SMART SM00397 tSNARE_6 20 87 7.2E-19
5 g959.t16 SUPERFAMILY SSF47661 t-snare proteins 1 80 4.55E-27
10 g959.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 120 -

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