General information for g10901.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable Golgi SNAP receptor complex member 2.
Parent gene
- The parent gene g10901 is located on chr_1: 12536865..12537612 (- strand)
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.t4 | TTS | g10901.t4 | 12536846 | 12536846 |
| chr_1 | g10901 | g10901.t4 | isoform | g10901.t4 | 12536865 | 12537612 |
| chr_1 | g10901 | g10901.t4 | exon | g10901.t4.exon1 | 12536865 | 12537275 |
| chr_1 | g10901 | g10901.t4 | cds | g10901.t4.CDS1 | 12536865 | 12537215 |
| chr_1 | g10901 | g10901.t4 | exon | g10901.t4.exon2 | 12537317 | 12537422 |
| chr_1 | g10901 | g10901.t4 | exon | g10901.t4.exon3 | 12537479 | 12537612 |
| chr_1 | g10901 | g10901.t4 | TSS | g10901.t4 | 12537683 | 12537683 |
Sequences
>g10901.t4 Gene=g10901 Length=651
ATGGATGCATTATATCATTCAACTAACAAAATAATTCACGAAATACAGCAGTGTTTTCAA
CAGCTAAATAACCCCGGGGTAGATTCAATTGCTGTAGAAAATGAAATTATGACGAAAATA
AATACGGTGAATGCCAACTGCGACCGCCTCGATGTTCTCGTATTTAAAGTACCAGCAGCA
ACTCGCCAGAACTCAAAAATGAAAGTTGATCAGCTAAAATACGACATTCGACACTTGCAA
ATATCAATAAAATTTTAGACCGCTTTGAGCATGTATCAACAAAAGAGACAAAAAAGAGAA
ATGGAAGCTACAGAAAGAGAACAATTATTAACAAGAAGATTTCAGCCTAATTCAGAAACA
ACTATAGATCTTGACTATTCACTTCAACACAATACACAAATGCAAAATGCACATAGAGGC
GTAGATGAAATGCTTTCTACTGGCAATAATATAATTAATAGTTTAAGAAATCAACGAGAT
ATATTGAAAGGTGCTCGTACTAGAATGTTGAATGTTGGTAGCACGCTTGGTCTTTCAGAC
CATACAATAAGGCTAATTGAGAGGAGACTGACAGATGATCGATATGTTATGTTTGCAGGA
ATGTTTGTTACATTATGTATTATTGGCTTAGTTATTTATCTATTAGCTTAA
>g10901.t4 Gene=g10901 Length=116
MEATEREQLLTRRFQPNSETTIDLDYSLQHNTQMQNAHRGVDEMLSTGNNIINSLRNQRD
ILKGARTRMLNVGSTLGLSDHTIRLIERRLTDDRYVMFAGMFVTLCIIGLVIYLLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10901.t4 | CDD | cd15863 | SNARE_GS27 | 25 | 89 | 3.60056E-27 |
| 6 | g10901.t4 | Gene3D | G3DSA:1.20.5.110 | - | 19 | 94 | 1.9E-8 |
| 2 | g10901.t4 | PANTHER | PTHR21230 | VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED | 1 | 113 | 2.5E-33 |
| 3 | g10901.t4 | PANTHER | PTHR21230:SF1 | GOLGI SNAP RECEPTOR COMPLEX MEMBER 2 | 1 | 113 | 2.5E-33 |
| 1 | g10901.t4 | Pfam | PF12352 | Snare region anchored in the vesicle membrane C-terminus | 26 | 90 | 7.4E-18 |
| 7 | g10901.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 94 | - |
| 9 | g10901.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 95 | 115 | - |
| 8 | g10901.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 116 | 116 | - |
| 5 | g10901.t4 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 29 | 85 | 4.34E-9 |
| 4 | g10901.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 115 | - |
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.
