General information for g1766.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein SEC13-like protein.
Parent gene
- The parent gene g1766 is located on chr_3: 12901777..12902621 (+ 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 | g1766 | g1766.t11 | TSS | g1766.t11 | 12901499 | 12901499 |
| chr_3 | g1766 | g1766.t11 | isoform | g1766.t11 | 12901777 | 12902621 |
| chr_3 | g1766 | g1766.t11 | exon | g1766.t11.exon1 | 12901777 | 12902621 |
| chr_3 | g1766 | g1766.t11 | cds | g1766.t11.CDS1 | 12902071 | 12902607 |
| chr_3 | g1766 | g1766.t11 | TTS | g1766.t11 | 12902679 | 12902679 |
Sequences
>g1766.t11 Gene=g1766 Length=845
ATTAAAAACGGTGGACAGCGCCTTAAAGCTGATTTAAAAGGGCATGCTGGTCCTGTATGG
CAAATCACATGGGCTCATCCGCGTTTTGGAAATATTTTAGCATCTTGCTCTTACGACCGG
AAAGTTATTTTATGGAAGGAAACAAATGGAGAATGGACAAAGTATTATGAATATAATAAT
CATGATTCATCAGTTAATAGCGTTTCATTTGCGCCACCTGAATATGGCTTAATTTTGGCT
TGTGGCAGTTCTGATGGGTCTATTTCTATTTTGACCTGTAATACAGAAACGGGAATGTTT
GATGTGAAAAAGATTCCAAATGCTCATACAATTGGTTGCAACGCATTAAGTTGGTGTCCT
TCTGCACTTCCAGATTCGACATTCGATCAAAAAGGCAAACAAACAAACCCTAATAATGGA
GTTGCTGCACAAATAAAACGATTCGCATCTGGAGGATGTGACAATGCAGTTAAAATTTGG
AAGGAAGATGGTGATCGCTGGATTGAAGAGCACAAACTTGAAGTTCATTGCGATTGGATT
CGCGATGTTGCTTGGGCACCATCAATTGGATTGCCATCAACTCGTATTGCAAGCTGCTCA
CAAGATCGTCGCGTAATTATTTGGAGCACTGAAGATTTTGCCTTGTGGACTCCAACAATC
TTAAATACTTTTGATGATGTTGTATGGAACGTGAGTTGGTCATTGACTGGTAATGTTTTA
GGTGTGTCAGGTGGAGACAACAAGATATTTTTATACAAAGAGAATAATGATGGAATTTGG
TCATGTATCAGTGAAGATGCAGAAAATGCTAAAGATGTTAGACATACATAAGGAAAACAA
TTCAT
>g1766.t11 Gene=g1766 Length=178
MFDVKKIPNAHTIGCNALSWCPSALPDSTFDQKGKQTNPNNGVAAQIKRFASGGCDNAVK
IWKEDGDRWIEEHKLEVHCDWIRDVAWAPSIGLPSTRIASCSQDRRVIIWSTEDFALWTP
TILNTFDDVVWNVSWSLTGNVLGVSGGDNKIFLYKENNDGIWSCISEDAENAKDVRHT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1766.t11 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 169 | 0.00000 |
| 2 | g1766.t11 | PANTHER | PTHR11024:SF2 | PROTEIN SEC13 HOMOLOG | 2 | 167 | 0.00000 |
| 3 | g1766.t11 | PANTHER | PTHR11024 | NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER | 2 | 167 | 0.00000 |
| 1 | g1766.t11 | Pfam | PF00400 | WD domain, G-beta repeat | 73 | 111 | 0.01900 |
| 9 | g1766.t11 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 50 | 164 | 11.23400 |
| 7 | g1766.t11 | SMART | SM00320 | WD40_4 | 1 | 63 | 0.46000 |
| 6 | g1766.t11 | SMART | SM00320 | WD40_4 | 68 | 111 | 0.00059 |
| 5 | g1766.t11 | SMART | SM00320 | WD40_4 | 119 | 155 | 0.76000 |
| 4 | g1766.t11 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 9 | 159 | 0.00000 |
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:1904263 | positive regulation of TORC1 signaling | BP |
| GO:0005515 | protein binding | MF |
| GO:0030127 | COPII vesicle coat | CC |
| GO:0090114 | COPII-coated vesicle budding | BP |
| GO:0005198 | structural molecule activity | MF |
| GO:0016192 | vesicle-mediated transport | BP |
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.
