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.t8 isoform g959.t8 7041650 7060460
chr_3 g959 g959.t8 exon g959.t8.exon1 7041650 7042295
chr_3 g959 g959.t8 cds g959.t8.CDS1 7042263 7042295
chr_3 g959 g959.t8 exon g959.t8.exon2 7051815 7052006
chr_3 g959 g959.t8 cds g959.t8.CDS2 7051815 7052006
chr_3 g959 g959.t8 exon g959.t8.exon3 7052193 7052249
chr_3 g959 g959.t8 cds g959.t8.CDS3 7052193 7052249
chr_3 g959 g959.t8 exon g959.t8.exon4 7052347 7052530
chr_3 g959 g959.t8 cds g959.t8.CDS4 7052347 7052530
chr_3 g959 g959.t8 exon g959.t8.exon5 7052601 7052674
chr_3 g959 g959.t8 cds g959.t8.CDS5 7052601 7052674
chr_3 g959 g959.t8 exon g959.t8.exon6 7052753 7052890
chr_3 g959 g959.t8 cds g959.t8.CDS6 7052753 7052890
chr_3 g959 g959.t8 exon g959.t8.exon7 7053118 7053228
chr_3 g959 g959.t8 cds g959.t8.CDS7 7053118 7053228
chr_3 g959 g959.t8 exon g959.t8.exon8 7060239 7060460
chr_3 g959 g959.t8 cds g959.t8.CDS8 7060239 7060316
chr_3 g959 g959.t8 TTS g959.t8 7060535 7060535
chr_3 g959 g959.t8 TSS g959.t8 NA NA

Sequences

>g959.t8 Gene=g959 Length=1624
TTCTTAACAGTCTAGTATATTTTCAAAGTTCAATTGTATATTAGTATCTCAAAAGTAATG
TTTATACTTGCTTATACTCTTATGTATGGGAGAAGACTTAGTGTTGTGATTAATCGTGTA
AAATGATAATTTTCAGAGACTTTCTATAGTGAAAAATTAATTATTTCTAATTTTTGATTA
CTCTTAACTATCTAAGAATGAGTGATTGAGTGACAAGCATTCTACTGCATATAGTGATTT
GATAAAACATCGTGTTGCTCTTAACTTAAGAATTTGTTCATGCGCAAATAGTCGAAAAGA
AAATCAATAAAATCGTGAAAAAAACCTTCGCGATTTGTGGAGAATTTGTGCTGAAATTAA
TGTTTTAGCGTGAATAAATCATAAATAAAAATCAATGGAAGCCTAGTGAATACTAAATAG
TATTTAAATATCATAAGGGTTTTAGTGAAAAGTGTGTAAATTCTGAAATTTGGAAAGTTT
TCATTTCTGTAAGGCTGCTTGAAGAAAAGAAGAGAGTGCGAGAGAACGAAAAAATTGCAA
AATCCCAAAGTTGATTTTCAAAGCATCAAACGACTGCCTCAACAAATATTGAAATACAAC
ATTAAAAAGCATCATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGA
CGAGGATGCGGGGATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTT
CACTGAGGTGGAAGAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGT
TAAGAAAAAACACAGTTCCATCTTATCCGCTCCTCAAACGGATGAAAGTAAGTTGTGTAT
TTTTTTTAATGAAAACTTTGTGAATGATGCCAATAGAGTTAGAGGAAAACTAAAGAATAT
CGAACAAAGTATCGAGCAAGAAGAGCAGAGTAAATCAGCAAGTGCCGATTTACGAATACG
TAAGACACAACATTCGACATTATCACGAAAATTTGTCGAAGTAATGACAGAATATAATCG
AACACAAACTGATTATCGAGAGAGATGTAAAGCGAGAATACAACGTCAATTGGAAATCAC
TGGTAAAGCCACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCGGCAGT
GTTTACACAAGGAATTATTATGGAAACACAACAAGCAAAACAGACCCTGGCAGATATCGA
AGCACGACATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGCACGATATGTT
CATGGATATGGCAATGTTGGTCGAGAGTCAGGGTGAAATGATTGATCGTATAGAGTATCA
TGTTGAGCATGCAATGGATTATGTCCAAACAGCTACACAAGATACCAAAAAAGCACTCAA
ATACCAAAGTAAAGCTCGTCGGAAAAAAATTTATATCATAATCTGCCTGACGATAGTAGG
AATTCTATTGCTATTGTATCTATACAGTCTCATCTTTTGATTGGAATAACTGCCACTTCA
GCAAAAAACACAACGACTATTTATGATGTCATCTATCTAATCTATATAATTTTTTGTTCT
ACAAGTTGTCATTATACTTTTATATGTATATTTGTCATCGAAGTATCCTTTTTATTGCAT
TGTT

>g959.t8 Gene=g959 Length=288
MTKDRLAALHAAQSDDEDAGMDEVAINVDGFMEEFFTEVEEVREMIDKIQYNVEEVKKKH
SSILSAPQTDESKLCIFFNENFVNDANRVRGKLKNIEQSIEQEEQSKSASADLRIRKTQH
STLSRKFVEVMTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFTQG
IIMETQQAKQTLADIEARHADIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYHVEHA
MDYVQTATQDTKKALKYQSKARRKKIYIIICLTIVGILLLLYLYSLIF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g959.t8 CDD cd00179 SynN 43 181 3.66648E-42
14 g959.t8 CDD cd15880 SNARE_syntaxin1 191 259 6.15874E-38
9 g959.t8 Coils Coil Coil 39 59 -
8 g959.t8 Coils Coil Coil 86 106 -
6 g959.t8 Gene3D G3DSA:1.20.58.70 - 31 153 1.8E-45
7 g959.t8 Gene3D G3DSA:1.20.5.110 - 180 287 3.2E-42
3 g959.t8 PANTHER PTHR19957:SF84 SYNTAXIN-1A 20 280 8.5E-116
4 g959.t8 PANTHER PTHR19957 SYNTAXIN 20 280 8.5E-116
1 g959.t8 Pfam PF00804 Syntaxin 32 227 8.7E-57
2 g959.t8 Pfam PF05739 SNARE domain 228 280 2.5E-18
10 g959.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 265 -
12 g959.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 266 287 -
11 g959.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 288 288 -
18 g959.t8 ProSitePatterns PS00914 Syntaxin / epimorphin family signature. 198 237 -
19 g959.t8 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 192 254 20.749
16 g959.t8 SMART SM00503 SynN_4 27 146 1.1E-29
17 g959.t8 SMART SM00397 tSNARE_6 187 254 4.3E-21
5 g959.t8 SUPERFAMILY SSF47661 t-snare proteins 30 247 2.88E-60
15 g959.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 266 287 -

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

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.

Raw TPM values