General information for g10901.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g10901.t1 | 12536846 | 12536846 |
| chr_1 | g10901 | g10901.t1 | isoform | g10901.t1 | 12536865 | 12537612 |
| chr_1 | g10901 | g10901.t1 | exon | g10901.t1.exon1 | 12536865 | 12537257 |
| chr_1 | g10901 | g10901.t1 | cds | g10901.t1.CDS1 | 12536865 | 12537257 |
| chr_1 | g10901 | g10901.t1 | exon | g10901.t1.exon2 | 12537317 | 12537422 |
| chr_1 | g10901 | g10901.t1 | cds | g10901.t1.CDS2 | 12537317 | 12537422 |
| chr_1 | g10901 | g10901.t1 | exon | g10901.t1.exon3 | 12537479 | 12537612 |
| chr_1 | g10901 | g10901.t1 | cds | g10901.t1.CDS3 | 12537479 | 12537612 |
| chr_1 | g10901 | g10901.t1 | TSS | g10901.t1 | 12537683 | 12537683 |
Sequences
>g10901.t1 Gene=g10901 Length=633
ATGGATGCATTATATCATTCAACTAACAAAATAATTCACGAAATACAGCAGTGTTTTCAA
CAGCTAAATAACCCCGGGGTAGATTCAATTGCTGTAGAAAATGAAATTATGACGAAAATA
AATACGGTGAATGCCAACTGCGACCGCCTCGATGTTCTCGTATTTAAAGTACCAGCAGCA
ACTCGCCAGAACTCAAAAATGAAAGTTGATCAGCTAAAATACGACATTCGACACTTGCAA
ACCGCTTTGAGCATGTATCAACAAAAGAGACAAAAAAGAGAAATGGAAGCTACAGAAAGA
GAACAATTATTAACAAGAAGATTTCAGCCTAATTCAGAAACAACTATAGATCTTGACTAT
TCACTTCAACACAATACACAAATGCAAAATGCACATAGAGGCGTAGATGAAATGCTTTCT
ACTGGCAATAATATAATTAATAGTTTAAGAAATCAACGAGATATATTGAAAGGTGCTCGT
ACTAGAATGTTGAATGTTGGTAGCACGCTTGGTCTTTCAGACCATACAATAAGGCTAATT
GAGAGGAGACTGACAGATGATCGATATGTTATGTTTGCAGGAATGTTTGTTACATTATGT
ATTATTGGCTTAGTTATTTATCTATTAGCTTAA
>g10901.t1 Gene=g10901 Length=210
MDALYHSTNKIIHEIQQCFQQLNNPGVDSIAVENEIMTKINTVNANCDRLDVLVFKVPAA
TRQNSKMKVDQLKYDIRHLQTALSMYQQKRQKREMEATEREQLLTRRFQPNSETTIDLDY
SLQHNTQMQNAHRGVDEMLSTGNNIINSLRNQRDILKGARTRMLNVGSTLGLSDHTIRLI
ERRLTDDRYVMFAGMFVTLCIIGLVIYLLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10901.t1 | CDD | cd15863 | SNARE_GS27 | 119 | 183 | 3.35978E-27 |
| 5 | g10901.t1 | Gene3D | G3DSA:1.20.5.110 | - | 117 | 188 | 5.3E-8 |
| 2 | g10901.t1 | PANTHER | PTHR21230 | VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED | 3 | 207 | 4.3E-62 |
| 3 | g10901.t1 | PANTHER | PTHR21230:SF1 | GOLGI SNAP RECEPTOR COMPLEX MEMBER 2 | 3 | 207 | 4.3E-62 |
| 9 | g10901.t1 | PIRSF | PIRSF028865 | Membrin-2 | 1 | 210 | 3.2E-65 |
| 1 | g10901.t1 | Pfam | PF12352 | Snare region anchored in the vesicle membrane C-terminus | 120 | 184 | 2.9E-17 |
| 6 | g10901.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 188 | - |
| 8 | g10901.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 189 | 209 | - |
| 7 | g10901.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 210 | 210 | - |
| 4 | g10901.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 123 | 179 | 1.62E-8 |
| 11 | g10901.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 190 | 209 | - |
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:0005484 | SNAP receptor activity | MF |
| GO:0005794 | Golgi apparatus | CC |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K08496 (golgi SNAP receptor complex member 2)
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.
