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.t14 isoform g959.t14 7051825 7053237
chr_3 g959 g959.t14 exon g959.t14.exon1 7051825 7051995
chr_3 g959 g959.t14 exon g959.t14.exon2 7052074 7052128
chr_3 g959 g959.t14 exon g959.t14.exon3 7052328 7052530
chr_3 g959 g959.t14 cds g959.t14.CDS1 7052455 7052530
chr_3 g959 g959.t14 exon g959.t14.exon4 7052601 7052674
chr_3 g959 g959.t14 cds g959.t14.CDS2 7052601 7052674
chr_3 g959 g959.t14 exon g959.t14.exon5 7052753 7053237
chr_3 g959 g959.t14 cds g959.t14.CDS3 7052753 7053001
chr_3 g959 g959.t14 TSS g959.t14 NA NA
chr_3 g959 g959.t14 TTS g959.t14 NA NA

Sequences

>g959.t14 Gene=g959 Length=988
ATGACGAGGATGCGGGGATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGT
TTTTCACTGAGGTGGAAGAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAG
AGGTTAAGAAAAAACACAGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGC
AAGAGTTAGAGGATCTGATGGCAGATATTAAGAAAAATGCCAATAGATCATACAAATAAA
TATAGAATATCGAACAAAGTATCGAGCAAGAAGAGCAGAGTAAATCAGCAAGTGCCGATT
TACGAATACGTAAGACACAACATTCGACATTATCACGAAAATTTGTCGAAGTAATGACAG
AATATAATCGAACACAAACTGATTATCGAGAGAGATGTAAAGCGAGAATACAACGTCAAT
TGGAAATCACTGGTAAAGCCACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAA
ATTCGGCAGTGTTTACACAAGGAATTATTATGGAAACACAACAAGCAAAACAGACCCTGG
CAGATATCGAAGCACGACATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGC
ACGATATGTTCATGGATATGGCAATGTTGGTCGAGAGTCAGGTAATGAAAAATGAATTGA
GTTCTGTTTTTTTTTGTTTTAGAGACTTTGGTGTTATTGTGTGCTGTCATTTTTCGTTTA
TGTTTATGTCATCGATAATGAAATTTAATTAATTCAAAATATTTTCTTTCTCTTTTCTCT
TCCTTTAAACTTTATTATTGATATTTCAATTTAAAAATGTTTTATTGTTTGTAAAAAAAA
ACTTTTTATTAAATTATGAAAAATATAGGGTGAAATGATTGATCGTATAGAGTATCATGT
TGAGCATGCAATGGATTATGTCCAAACAGCTACACAAGATACCAAAAAAGCACTCAAATA
CCAAAGTAAAGCTCGTCGGGTAAGTTGA

>g959.t14 Gene=g959 Length=132
MTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFTQGIIMETQQAKQ
TLADIEARHADIIKLENSIRELHDMFMDMAMLVESQVMKNELSSVFFCFRDFGVIVCCHF
SFMFMSSIMKFN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g959.t14 CDD cd15848 SNARE_syntaxin1-like 61 96 1.04394E-19
5 g959.t14 Gene3D G3DSA:1.20.58.70 - 1 99 1.1E-42
2 g959.t14 PANTHER PTHR19957:SF231 SYNTAXIN-1A HOMOLOG 1 97 8.2E-50
3 g959.t14 PANTHER PTHR19957 SYNTAXIN 1 97 8.2E-50
1 g959.t14 Pfam PF00804 Syntaxin 1 96 1.3E-36
6 g959.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 106 -
8 g959.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 129 -
7 g959.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 130 132 -
11 g959.t14 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 62 96 9.823
4 g959.t14 SUPERFAMILY SSF47661 t-snare proteins 1 96 3.18E-30
10 g959.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 106 128 -

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: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