Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t15 isoform g959.t15 7052231 7060460
chr_3 g959 g959.t15 exon g959.t15.exon1 7052231 7052249
chr_3 g959 g959.t15 exon g959.t15.exon2 7052347 7052530
chr_3 g959 g959.t15 cds g959.t15.CDS1 7052455 7052530
chr_3 g959 g959.t15 exon g959.t15.exon3 7052601 7052674
chr_3 g959 g959.t15 cds g959.t15.CDS2 7052601 7052674
chr_3 g959 g959.t15 exon g959.t15.exon4 7052753 7052890
chr_3 g959 g959.t15 cds g959.t15.CDS3 7052753 7052890
chr_3 g959 g959.t15 exon g959.t15.exon5 7053118 7053228
chr_3 g959 g959.t15 cds g959.t15.CDS4 7053118 7053228
chr_3 g959 g959.t15 exon g959.t15.exon6 7060239 7060460
chr_3 g959 g959.t15 cds g959.t15.CDS5 7060239 7060316
chr_3 g959 g959.t15 TTS g959.t15 7060535 7060535
chr_3 g959 g959.t15 TSS g959.t15 NA NA

Sequences

>g959.t15 Gene=g959 Length=748
AGTTAGAGGAAAACTAAAGAATATCGAACAAAGTATCGAGCAAGAAGAGCAGAGTAAATC
AGCAAGTGCCGATTTACGAATACGTAAGACACAACATTCGACATTATCACGAAAATTTGT
CGAAGTAATGACAGAATATAATCGAACACAAACTGATTATCGAGAGAGATGTAAAGCGAG
AATACAACGTCAATTGGAAATCACTGGTAAAGCCACAACAAATGAAGAACTCGAAGAAAT
GTTGGAGCAAGGAAATTCGGCAGTGTTTACACAAGGAATTATTATGGAAACACAACAAGC
AAAACAGACCCTGGCAGATATCGAAGCACGACATGCTGATATCATTAAACTTGAAAACTC
AATTCGAGAATTGCACGATATGTTCATGGATATGGCAATGTTGGTCGAGAGTCAGGGTGA
AATGATTGATCGTATAGAGTATCATGTTGAGCATGCAATGGATTATGTCCAAACAGCTAC
ACAAGATACCAAAAAAGCACTCAAATACCAAAGTAAAGCTCGTCGGAAAAAAATTTATAT
CATAATCTGCCTGACGATAGTAGGAATTCTATTGCTATTGTATCTATACAGTCTCATCTT
TTGATTGGAATAACTGCCACTTCAGCAAAAAACACAACGACTATTTATGATGTCATCTAT
CTAATCTATATAATTTTTTGTTCTACAAGTTGTCATTATACTTTTATATGTATATTTGTC
ATCGAAGTATCCTTTTTATTGCATTGTT

>g959.t15 Gene=g959 Length=158
MTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFTQGIIMETQQAKQ
TLADIEARHADIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYHVEHAMDYVQTATQD
TKKALKYQSKARRKKIYIIICLTIVGILLLLYLYSLIF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g959.t15 CDD cd15880 SNARE_syntaxin1 61 129 6.75132E-39
6 g959.t15 Gene3D G3DSA:1.20.58.70 - 1 117 1.8E-55
3 g959.t15 PANTHER PTHR19957:SF84 SYNTAXIN-1A 1 150 2.0E-75
4 g959.t15 PANTHER PTHR19957 SYNTAXIN 1 150 2.0E-75
1 g959.t15 Pfam PF00804 Syntaxin 1 97 1.5E-37
2 g959.t15 Pfam PF05739 SNARE domain 98 150 8.4E-19
7 g959.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 135 -
9 g959.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 157 -
8 g959.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 158 158 -
12 g959.t15 ProSitePatterns PS00914 Syntaxin / epimorphin family signature. 68 107 -
14 g959.t15 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 62 124 20.749
13 g959.t15 SMART SM00397 tSNARE_6 57 124 4.3E-21
5 g959.t15 SUPERFAMILY SSF47661 t-snare proteins 1 117 3.41E-41
11 g959.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 157 -

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:0000149 SNARE binding MF
GO:0017157 regulation of exocytosis BP
GO:0016021 integral component of membrane CC
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