General information for g2589.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Golgi SNAP receptor complex member 1.
Parent gene
- The parent gene g2589 is located on chr_3: 18926744..18928552 (+ 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_3 | g2589 | g2589.t3 | TSS | g2589.t3 | 18926612 | 18926612 |
| chr_3 | g2589 | g2589.t3 | isoform | g2589.t3 | 18926744 | 18928552 |
| chr_3 | g2589 | g2589.t3 | exon | g2589.t3.exon1 | 18926744 | 18926762 |
| chr_3 | g2589 | g2589.t3 | cds | g2589.t3.CDS1 | 18926744 | 18926762 |
| chr_3 | g2589 | g2589.t3 | exon | g2589.t3.exon2 | 18926833 | 18927253 |
| chr_3 | g2589 | g2589.t3 | cds | g2589.t3.CDS2 | 18926833 | 18927253 |
| chr_3 | g2589 | g2589.t3 | exon | g2589.t3.exon3 | 18927314 | 18927647 |
| chr_3 | g2589 | g2589.t3 | cds | g2589.t3.CDS3 | 18927314 | 18927551 |
| chr_3 | g2589 | g2589.t3 | exon | g2589.t3.exon4 | 18928509 | 18928552 |
| chr_3 | g2589 | g2589.t3 | TTS | g2589.t3 | NA | NA |
Sequences
>g2589.t3 Gene=g2589 Length=818
ATGGCAGAGACATGGGATGAAATACGTAAAAAGTCAAGACTATTGGAAAATGAATTAGAT
CTCAAACTTGTAAGTTTGAGCAAAATATCATCAGGAAATAGCTTTGGCGGTGAAAATTCT
CCATTACTTTCAAGTGAATTTTCTTTTGATACGATCTCACTTGAAGTTAATGATATGCTG
GCAAAATTAAGCGAATTGAATGAAAAAATGGCACAAATGAAACCCAGTGGAACAGCAATG
ATACACACTCAATCGAGACATCGTGATATTCTAAACTCTTACCGGACAGAATTTAATAAA
ATTATCCAAAATCATAATTTAAAAGTAGAAAGAGAAGCATTATTATCAAATTCGGGACTT
TTGAATTCACCATCAAACAATAGCTCATCATCGCTTAGTCGTCGAGACATGTATTTAAAG
GAAAGCCAACATTTATCAAATAGTCACAATATGGTCAATGACCAGATATCTATTGCAATT
GAGACACAGAAGTCTTTGAAATCACAAAGAAAGGCATTCAAACGGTTACAAAATCGATTC
AATAATCTTGCCAATAATTTTCCAAGAATAAATTCATTGGTGCAGAGAATTAATATAAAG
AAAAAGCGAGACAGTCTGATAATTGCATCTGTAATTGCGGCTTGCACAATATTAATGCTT
CTTTATGCATTTCATTAAAAACGAAATGAATTTCACAGAAGTAATTATCAACATTCAATT
ATTTTCTTATTTAAAGAGAAAGTTATTAAATTATTATCGTTTTTTAAACTACTTTACCCT
ATATGTATATATATTTGAACTAATACACAAAGTTAAAA
>g2589.t3 Gene=g2589 Length=225
MAETWDEIRKKSRLLENELDLKLVSLSKISSGNSFGGENSPLLSSEFSFDTISLEVNDML
AKLSELNEKMAQMKPSGTAMIHTQSRHRDILNSYRTEFNKIIQNHNLKVEREALLSNSGL
LNSPSNNSSSSLSRRDMYLKESQHLSNSHNMVNDQISIAIETQKSLKSQRKAFKRLQNRF
NNLANNFPRINSLVQRINIKKKRDSLIIASVIAACTILMLLYAFH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2589.t3 | Coils | Coil | Coil | 166 | 186 | - |
| 2 | g2589.t3 | PANTHER | PTHR21094 | GOS-28 SNARE- RELATED | 3 | 225 | 6.4E-54 |
| 3 | g2589.t3 | PANTHER | PTHR21094:SF0 | GOLGI SNAP RECEPTOR COMPLEX MEMBER 1 | 3 | 225 | 6.4E-54 |
| 9 | g2589.t3 | PIRSF | PIRSF027109 | Golgi_SNARE | 1 | 225 | 5.9E-53 |
| 1 | g2589.t3 | Pfam | PF12352 | Snare region anchored in the vesicle membrane C-terminus | 136 | 201 | 3.7E-20 |
| 6 | g2589.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 205 | - |
| 8 | g2589.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 206 | 224 | - |
| 7 | g2589.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 225 | 225 | - |
| 4 | g2589.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 224 | - |
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:0016021 | integral component of membrane | CC |
| GO:0006888 | endoplasmic reticulum to Golgi vesicle-mediated transport | BP |
| GO:0005801 | cis-Golgi network | CC |
| GO:0000139 | Golgi membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K08495 (golgi SNAP receptor complex member 1)
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.
