General information for g5882.t257
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as WD repeat-containing protein 82.
Parent gene
- The parent gene g5882 is located on chr_2: 12573531..12574934 (- 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_2 | g5882 | g5882.t257 | TTS | g5882.t257 | 12572810 | 12572810 |
| chr_2 | g5882 | g5882.t257 | isoform | g5882.t257 | 12573531 | 12574043 |
| chr_2 | g5882 | g5882.t257 | exon | g5882.t257.exon1 | 12573531 | 12573775 |
| chr_2 | g5882 | g5882.t257 | cds | g5882.t257.CDS1 | 12573531 | 12573775 |
| chr_2 | g5882 | g5882.t257 | exon | g5882.t257.exon2 | 12573838 | 12574043 |
| chr_2 | g5882 | g5882.t257 | cds | g5882.t257.CDS2 | 12573838 | 12573976 |
| chr_2 | g5882 | g5882.t257 | TSS | g5882.t257 | 12574711 | 12574711 |
Sequences
>g5882.t257 Gene=g5882 Length=451
AGTTAATTCTGAATCAATTAAATTGTACGATTTAAGATCATATGATAAAGGACCATTTGT
TACTTTTATGCTAAATCAAGAAAAAGAATGCGAGTGGACTGGATTAAAATTTTCAAAAGA
TGGAAAGACAATTTTAATTAGCACAAATGGCTCAGTTATTCGTTTGATTGATGCATTTCA
CGGAACACCACTTCAAACTTTTACGGGATATTTAAACAATAAAGGAATACCAATTGAGGC
GTCATTCAGTCCAGATTCACAATACATTTTTTCGGGTAGTACTGATGGACGTGTGCACGT
GTGGAATGCAGATACTGGTTTTAAAGTTTGTGTTCTTAATGGTGATCATCCAAGTCCTGT
ACAATGTATTCAATTTAATCCGAAATACATGATGATGGTTTCAGCATGTACTAATTTAGC
TTTTTGGCTGCCGACTATTGAAGAAGAATAA
>g5882.t257 Gene=g5882 Length=127
MLNQEKECEWTGLKFSKDGKTILISTNGSVIRLIDAFHGTPLQTFTGYLNNKGIPIEASF
SPDSQYIFSGSTDGRVHVWNADTGFKVCVLNGDHPSPVQCIQFNPKYMMMVSACTNLAFW
LPTIEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5882.t257 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 125 | 6.4E-22 |
| 2 | g5882.t257 | PANTHER | PTHR19861:SF0 | WD REPEAT-CONTAINING PROTEIN 82 | 3 | 126 | 1.3E-43 |
| 3 | g5882.t257 | PANTHER | PTHR19861 | WD40 REPEAT PROTEIN SWD2 | 3 | 126 | 1.3E-43 |
| 1 | g5882.t257 | Pfam | PF00400 | WD domain, G-beta repeat | 39 | 80 | 5.2E-6 |
| 8 | g5882.t257 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 67 | 81 | - |
| 10 | g5882.t257 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 48 | 127 | 11.576 |
| 11 | g5882.t257 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 59 | 84 | 10.909 |
| 7 | g5882.t257 | SMART | SM00320 | WD40_4 | 3 | 35 | 260.0 |
| 6 | g5882.t257 | SMART | SM00320 | WD40_4 | 38 | 80 | 9.3E-4 |
| 5 | g5882.t257 | SMART | SM00320 | WD40_4 | 83 | 121 | 8.7 |
| 4 | g5882.t257 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 9 | 118 | 5.68E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5882/g5882.t257; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5882.t257.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0048188 | Set1C/COMPASS complex | CC |
| GO:0005515 | protein binding | MF |
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.
