Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable Golgi SNAP receptor complex member 2.

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 g10901 g10901.t2 TTS g10901.t2 12536846 12536846
chr_1 g10901 g10901.t2 isoform g10901.t2 12536865 12537255
chr_1 g10901 g10901.t2 exon g10901.t2.exon1 12536865 12537255
chr_1 g10901 g10901.t2 cds g10901.t2.CDS1 12536865 12537245
chr_1 g10901 g10901.t2 TSS g10901.t2 12537683 12537683

Sequences

>g10901.t2 Gene=g10901 Length=391
CGCTTTGAGCATGTATCAACAAAAGAGACAAAAAAGAGAAATGGAAGCTACAGAAAGAGA
ACAATTATTAACAAGAAGATTTCAGCCTAATTCAGAAACAACTATAGATCTTGACTATTC
ACTTCAACACAATACACAAATGCAAAATGCACATAGAGGCGTAGATGAAATGCTTTCTAC
TGGCAATAATATAATTAATAGTTTAAGAAATCAACGAGATATATTGAAAGGTGCTCGTAC
TAGAATGTTGAATGTTGGTAGCACGCTTGGTCTTTCAGACCATACAATAAGGCTAATTGA
GAGGAGACTGACAGATGATCGATATGTTATGTTTGCAGGAATGTTTGTTACATTATGTAT
TATTGGCTTAGTTATTTATCTATTAGCTTAA

>g10901.t2 Gene=g10901 Length=126
MYQQKRQKREMEATEREQLLTRRFQPNSETTIDLDYSLQHNTQMQNAHRGVDEMLSTGNN
IINSLRNQRDILKGARTRMLNVGSTLGLSDHTIRLIERRLTDDRYVMFAGMFVTLCIIGL
VIYLLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10901.t2 CDD cd15863 SNARE_GS27 35 99 8.6031E-27
6 g10901.t2 Gene3D G3DSA:1.20.5.110 - 29 104 2.4E-8
2 g10901.t2 PANTHER PTHR21230 VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED 2 123 3.4E-37
3 g10901.t2 PANTHER PTHR21230:SF1 GOLGI SNAP RECEPTOR COMPLEX MEMBER 2 2 123 3.4E-37
1 g10901.t2 Pfam PF12352 Snare region anchored in the vesicle membrane C-terminus 36 100 9.2E-18
7 g10901.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 104 -
9 g10901.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 105 125 -
8 g10901.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 126 126 -
5 g10901.t2 SUPERFAMILY SSF58038 SNARE fusion complex 39 95 5.23E-9
4 g10901.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 106 125 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed