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.t5 isoform g959.t5 7041650 7056627
chr_3 g959 g959.t5 exon g959.t5.exon1 7041650 7042295
chr_3 g959 g959.t5 exon g959.t5.exon2 7051815 7051995
chr_3 g959 g959.t5 exon g959.t5.exon3 7052074 7052128
chr_3 g959 g959.t5 exon g959.t5.exon4 7052329 7052530
chr_3 g959 g959.t5 cds g959.t5.CDS1 7052455 7052530
chr_3 g959 g959.t5 exon g959.t5.exon5 7052601 7052674
chr_3 g959 g959.t5 cds g959.t5.CDS2 7052601 7052674
chr_3 g959 g959.t5 exon g959.t5.exon6 7052753 7052890
chr_3 g959 g959.t5 cds g959.t5.CDS3 7052753 7052890
chr_3 g959 g959.t5 exon g959.t5.exon7 7053118 7053228
chr_3 g959 g959.t5 cds g959.t5.CDS4 7053118 7053228
chr_3 g959 g959.t5 exon g959.t5.exon8 7056281 7056627
chr_3 g959 g959.t5 cds g959.t5.CDS5 7056281 7056379
chr_3 g959 g959.t5 TTS g959.t5 7056612 7056612
chr_3 g959 g959.t5 TSS g959.t5 NA NA

Sequences

>g959.t5 Gene=g959 Length=1754
TTCTTAACAGTCTAGTATATTTTCAAAGTTCAATTGTATATTAGTATCTCAAAAGTAATG
TTTATACTTGCTTATACTCTTATGTATGGGAGAAGACTTAGTGTTGTGATTAATCGTGTA
AAATGATAATTTTCAGAGACTTTCTATAGTGAAAAATTAATTATTTCTAATTTTTGATTA
CTCTTAACTATCTAAGAATGAGTGATTGAGTGACAAGCATTCTACTGCATATAGTGATTT
GATAAAACATCGTGTTGCTCTTAACTTAAGAATTTGTTCATGCGCAAATAGTCGAAAAGA
AAATCAATAAAATCGTGAAAAAAACCTTCGCGATTTGTGGAGAATTTGTGCTGAAATTAA
TGTTTTAGCGTGAATAAATCATAAATAAAAATCAATGGAAGCCTAGTGAATACTAAATAG
TATTTAAATATCATAAGGGTTTTAGTGAAAAGTGTGTAAATTCTGAAATTTGGAAAGTTT
TCATTTCTGTAAGGCTGCTTGAAGAAAAGAAGAGAGTGCGAGAGAACGAAAAAATTGCAA
AATCCCAAAGTTGATTTTCAAAGCATCAAACGACTGCCTCAACAAATATTGAAATACAAC
ATTAAAAAGCATCATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGA
CGAGGATGCGGGGATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTT
CACTGAGGTGGAAGAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGT
TAAGAAAAAACACAGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGCAAGA
GTTAGAGGATCTGATGGCAGATATTAAGAAAAATGCCAATAGTCATACAAATAAATATAG
AATATCGAACAAAGTATCGAGCAAGAAGAGCAGAGTAAATCAGCAAGTGCCGATTTACGA
ATACGTAAGACACAACATTCGACATTATCACGAAAATTTGTCGAAGTAATGACAGAATAT
AATCGAACACAAACTGATTATCGAGAGAGATGTAAAGCGAGAATACAACGTCAATTGGAA
ATCACTGGTAAAGCCACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCG
GCAGTGTTTACACAAGGAATTATTATGGAAACACAACAAGCAAAACAGACCCTGGCAGAT
ATCGAAGCACGACATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGCACGAT
ATGTTCATGGATATGGCAATGTTGGTCGAGAGTCAGGGTGAAATGATTGATCGTATAGAG
TATCATGTTGAGCATGCAATGGATTATGTCCAAACAGCTACACAAGATACCAAAAAAGCA
CTCAAATACCAAAGTAAAGCTCGTCGGAAAAAGATATTGATTATAGCATGTTTGACTATA
GCGGCAGTGATTTTATTGATAATTTTAATCTTATACCTTATGAGTTTATTTGGAGCGACA
AATTAAACTCGACAAACAAATATAATATTAACAATTCTATACTAATCGCCATATCAACAA
AAATTCAAATTATATCAATTAAACAATGTCATGGACGTCAACACCTTTGGACTAGAGCAA
ATAACTTATATGCACATGGAGGAGGATGTTAAATTAGAATTAATTGTTGTAATTATAATT
TAAATAAGGCAATAGTTGGTGCGCATAAAATATGGATTATTAAATAAATTTTTCCTGCCA
CTTTTATTCGATTA

>g959.t5 Gene=g959 Length=165
MTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFTQGIIMETQQAKQ
TLADIEARHADIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYHVEHAMDYVQTATQD
TKKALKYQSKARRKKILIIACLTIAAVILLIILILYLMSLFGATN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g959.t5 CDD cd15880 SNARE_syntaxin1 61 129 3.44602E-39
6 g959.t5 Gene3D G3DSA:1.20.58.70 - 1 117 2.0E-55
3 g959.t5 PANTHER PTHR19957:SF231 SYNTAXIN-1A HOMOLOG 1 154 1.5E-75
4 g959.t5 PANTHER PTHR19957 SYNTAXIN 1 154 1.5E-75
1 g959.t5 Pfam PF00804 Syntaxin 1 97 1.7E-37
2 g959.t5 Pfam PF05739 SNARE domain 98 150 1.2E-15
7 g959.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 135 -
9 g959.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 158 -
8 g959.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 159 165 -
12 g959.t5 ProSitePatterns PS00914 Syntaxin / epimorphin family signature. 68 107 -
14 g959.t5 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 62 124 20.749
13 g959.t5 SMART SM00397 tSNARE_6 57 124 4.3E-21
5 g959.t5 SUPERFAMILY SSF47661 t-snare proteins 1 117 3.92E-41
11 g959.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 158 -

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