General information for g1593.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vesicle transport protein SEC20.
Parent gene
- The parent gene g1593 is located on chr_3: 12051871..12055337 (- 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 | g1593 | g1593.t1 | TTS | g1593.t1 | 12050956 | 12050956 |
| chr_3 | g1593 | g1593.t1 | isoform | g1593.t1 | 12051276 | 12052230 |
| chr_3 | g1593 | g1593.t1 | exon | g1593.t1.exon1 | 12051276 | 12051857 |
| chr_3 | g1593 | g1593.t1 | cds | g1593.t1.CDS1 | 12051276 | 12051857 |
| chr_3 | g1593 | g1593.t1 | exon | g1593.t1.exon2 | 12052162 | 12052230 |
| chr_3 | g1593 | g1593.t1 | cds | g1593.t1.CDS2 | 12052162 | 12052230 |
| chr_3 | g1593 | g1593.t1 | TSS | g1593.t1 | 12052321 | 12052321 |
Sequences
>g1593.t1 Gene=g1593 Length=651
ATGGAATCACAACGGCTACTAAAGCAAGAGATAATTGATCATAACTTACAAGTTAAAGCC
ATCATCCAGGACATTTTAGCATTTCGTGGATCATTACAAGACCTAGAATTGTTAAATGAA
GCAGGTAGAGCAAAACTTGCACAATTAAGGAAATGTATTGAGAAATTAGATGATTGGGCG
AGAGATGAAAATGATCCACAGCTCTCAAATGATGTCGACTCACATCGTGAACAATTTTCA
AAAACTTTGCAGGCATTTAGGAAAGCGAATATTAGCACAATGTTAGAAATAGAAAAGAGT
GATAAGGCGGAATTGTTTACAATTAAACCTGAAGCAGAACTTCGGCATAGAACTGCTAGT
AATCTAATATCACAACAAGAGAGTGTGACAGAACGTATGCTTAGTATATCAAGAAATTTG
GCTGAAACTACACAAAAATCAGCAGCAACTCTTGATTCACTTATTCAATCTTCATCAACT
GTCGATGGCACAAATGATGAATTATCGAACACAGCTGGTACAATTCAACAGTCAGGAAAA
TTACTCAACAAATATGGACGAAGGGAAACTACTGATAAAATTTTACTCTTCCTTGCATTC
TTCTTCTTTCTCGCTGTTGTGTTTTATATTGTGCAAAAGAGAATGTTTTAA
>g1593.t1 Gene=g1593 Length=216
MESQRLLKQEIIDHNLQVKAIIQDILAFRGSLQDLELLNEAGRAKLAQLRKCIEKLDDWA
RDENDPQLSNDVDSHREQFSKTLQAFRKANISTMLEIEKSDKAELFTIKPEAELRHRTAS
NLISQQESVTERMLSISRNLAETTQKSAATLDSLIQSSSTVDGTNDELSNTAGTIQQSGK
LLNKYGRRETTDKILLFLAFFFFLAVVFYIVQKRMF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g1593.t1 | PANTHER | PTHR12825:SF0 | VESICLE TRANSPORT PROTEIN SEC20 | 5 | 216 | 1.2E-39 |
| 3 | g1593.t1 | PANTHER | PTHR12825 | BNIP1-RELATED | 5 | 216 | 1.2E-39 |
| 1 | g1593.t1 | Pfam | PF03908 | Sec20 | 124 | 215 | 4.0E-27 |
| 5 | g1593.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 193 | - |
| 7 | g1593.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 194 | 211 | - |
| 6 | g1593.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 212 | 216 | - |
| 4 | g1593.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 194 | 211 | - |
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:0006890 | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | BP |
KEGG
Orthology
- This transcript has been annotated with K08497 (protein transport protein SEC20)
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.
