Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Syntaxin-42.

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_1 g13187 g13187.t2 TSS g13187.t2 28390046 28390046
chr_1 g13187 g13187.t2 isoform g13187.t2 28390867 28391230
chr_1 g13187 g13187.t2 exon g13187.t2.exon1 28390867 28391230
chr_1 g13187 g13187.t2 cds g13187.t2.CDS1 28390976 28391230
chr_1 g13187 g13187.t2 TTS g13187.t2 28391315 28391315

Sequences

>g13187.t2 Gene=g13187 Length=364
ATTAGATGAATATTTTCAAATTAAGCCAAATCAAAAGTTCAATCAGCAACATTTACTTCG
TTTAGAAGTTGATAACACAAAATTAGTTGAAGCACGAGAAAAAGAGGTGATGAATATTGT
GAAATCAATTGTGGATCTTAATCAAATTTACAAGGATTTATCGCATCTAGTTGAAGAGCA
AGGTACTGTTTTAGATAGAATCGATTATAATATTGAATCAACTCAAACACGCGTATATGA
GGGCTACAAACAACTGCAAAAAGCTGAACGCTATCAACGTGCAAATAGAAAAATGTATTG
CATATTTATTTTAGCCTCTGTGACATTGTTTATGATCATATTACTTATTATCGTAAAACT
ATAA

>g13187.t2 Gene=g13187 Length=84
MNIVKSIVDLNQIYKDLSHLVEEQGTVLDRIDYNIESTQTRVYEGYKQLQKAERYQRANR
KMYCIFILASVTLFMIILLIIVKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13187.t2 CDD cd15845 SNARE_syntaxin16 1 51 4.31085E-22
5 g13187.t2 Gene3D G3DSA:1.20.5.110 - 1 84 1.7E-28
2 g13187.t2 PANTHER PTHR19957 SYNTAXIN 2 76 3.6E-26
3 g13187.t2 PANTHER PTHR19957:SF83 SYNTAXIN-16 2 76 3.6E-26
1 g13187.t2 Pfam PF05739 SNARE domain 26 78 2.3E-19
6 g13187.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 62 -
8 g13187.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 63 82 -
7 g13187.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 84 -
12 g13187.t2 ProSiteProfiles PS50192 t-SNARE coiled-coil homology domain profile. 1 52 17.483
11 g13187.t2 SMART SM00397 tSNARE_6 1 52 9.1E-7
4 g13187.t2 SUPERFAMILY SSF58038 SNARE fusion complex 2 57 3.31E-18
10 g13187.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 82 -

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:0006886 intracellular protein transport BP
GO:0031201 SNARE complex CC

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