General information for g1766.t1
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.t1 | TSS | g1766.t1 | 12901499 | 12901499 |
| chr_3 | g1766 | g1766.t1 | isoform | g1766.t1 | 12901599 | 12902607 |
| chr_3 | g1766 | g1766.t1 | exon | g1766.t1.exon1 | 12901599 | 12901712 |
| chr_3 | g1766 | g1766.t1 | cds | g1766.t1.CDS1 | 12901599 | 12901712 |
| chr_3 | g1766 | g1766.t1 | exon | g1766.t1.exon2 | 12901768 | 12902607 |
| chr_3 | g1766 | g1766.t1 | cds | g1766.t1.CDS2 | 12901768 | 12902607 |
| chr_3 | g1766 | g1766.t1 | TTS | g1766.t1 | 12902679 | 12902679 |
Sequences
>g1766.t1 Gene=g1766 Length=954
ATGGTTAGCGTTCTTCAGACACTCGATAGCGGTCATGAGGACTTGATACACGGTGCAGAA
ATTGATTATTATGGACTTAATCTTGCAACATGTTCATCTGACAACACAATTAAGATTTTT
GACATTAAAAACGGTGGACAGCGCCTTAAAGCTGATTTAAAAGGGCATGCTGGTCCTGTA
TGGCAAATCACATGGGCTCATCCGCGTTTTGGAAATATTTTAGCATCTTGCTCTTACGAC
CGGAAAGTTATTTTATGGAAGGAAACAAATGGAGAATGGACAAAGTATTATGAATATAAT
AATCATGATTCATCAGTTAATAGCGTTTCATTTGCGCCACCTGAATATGGCTTAATTTTG
GCTTGTGGCAGTTCTGATGGGTCTATTTCTATTTTGACCTGTAATACAGAAACGGGAATG
TTTGATGTGAAAAAGATTCCAAATGCTCATACAATTGGTTGCAACGCATTAAGTTGGTGT
CCTTCTGCACTTCCAGATTCGACATTCGATCAAAAAGGCAAACAAACAAACCCTAATAAT
GGAGTTGCTGCACAAATAAAACGATTCGCATCTGGAGGATGTGACAATGCAGTTAAAATT
TGGAAGGAAGATGGTGATCGCTGGATTGAAGAGCACAAACTTGAAGTTCATTGCGATTGG
ATTCGCGATGTTGCTTGGGCACCATCAATTGGATTGCCATCAACTCGTATTGCAAGCTGC
TCACAAGATCGTCGCGTAATTATTTGGAGCACTGAAGATTTTGCCTTGTGGACTCCAACA
ATCTTAAATACTTTTGATGATGTTGTATGGAACGTGAGTTGGTCATTGACTGGTAATGTT
TTAGGTGTGTCAGGTGGAGACAACAAGATATTTTTATACAAAGAGAATAATGATGGAATT
TGGTCATGTATCAGTGAAGATGCAGAAAATGCTAAAGATGTTAGACATACATAA
>g1766.t1 Gene=g1766 Length=317
MVSVLQTLDSGHEDLIHGAEIDYYGLNLATCSSDNTIKIFDIKNGGQRLKADLKGHAGPV
WQITWAHPRFGNILASCSYDRKVILWKETNGEWTKYYEYNNHDSSVNSVSFAPPEYGLIL
ACGSSDGSISILTCNTETGMFDVKKIPNAHTIGCNALSWCPSALPDSTFDQKGKQTNPNN
GVAAQIKRFASGGCDNAVKIWKEDGDRWIEEHKLEVHCDWIRDVAWAPSIGLPSTRIASC
SQDRRVIIWSTEDFALWTPTILNTFDDVVWNVSWSLTGNVLGVSGGDNKIFLYKENNDGI
WSCISEDAENAKDVRHT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g1766.t1 | Gene3D | G3DSA:2.130.10.10 | - | 2 | 308 | 0.000000 |
| 5 | g1766.t1 | PANTHER | PTHR11024:SF2 | PROTEIN SEC13 HOMOLOG | 4 | 306 | 0.000000 |
| 6 | g1766.t1 | PANTHER | PTHR11024 | NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER | 4 | 306 | 0.000000 |
| 3 | g1766.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 6 | 41 | 0.028000 |
| 1 | g1766.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 52 | 87 | 0.003500 |
| 4 | g1766.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 97 | 131 | 0.130000 |
| 2 | g1766.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 212 | 250 | 0.049000 |
| 15 | g1766.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 9 | 303 | 21.331000 |
| 16 | g1766.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 53 | 96 | 9.673000 |
| 17 | g1766.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 99 | 131 | 8.503000 |
| 12 | g1766.t1 | SMART | SM00320 | WD40_4 | 1 | 41 | 0.000770 |
| 8 | g1766.t1 | SMART | SM00320 | WD40_4 | 46 | 87 | 0.000025 |
| 13 | g1766.t1 | SMART | SM00320 | WD40_4 | 92 | 133 | 0.013000 |
| 10 | g1766.t1 | SMART | SM00320 | WD40_4 | 140 | 202 | 0.460000 |
| 11 | g1766.t1 | SMART | SM00320 | WD40_4 | 207 | 250 | 0.000590 |
| 9 | g1766.t1 | SMART | SM00320 | WD40_4 | 258 | 294 | 0.760000 |
| 7 | g1766.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 14 | 300 | 0.000000 |
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 transcript has been annotated with K14004 (protein transport protein SEC13)
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.
