General information for g5882.t258
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.t258 | TTS | g5882.t258 | 12572810 | 12572810 |
| chr_2 | g5882 | g5882.t258 | isoform | g5882.t258 | 12573531 | 12574611 |
| chr_2 | g5882 | g5882.t258 | exon | g5882.t258.exon1 | 12573531 | 12574309 |
| chr_2 | g5882 | g5882.t258 | cds | g5882.t258.CDS1 | 12573797 | 12574309 |
| chr_2 | g5882 | g5882.t258 | exon | g5882.t258.exon2 | 12574384 | 12574611 |
| chr_2 | g5882 | g5882.t258 | cds | g5882.t258.CDS2 | 12574384 | 12574611 |
| chr_2 | g5882 | g5882.t258 | TSS | g5882.t258 | 12574711 | 12574711 |
Sequences
>g5882.t258 Gene=g5882 Length=1007
ATGAAGTTAAACGATCCAGTAATTCGTAGCTTTAAAGTGGCAAAAGTATTTCGTGAAAAT
CAAGATAAATTAAATTCTATAGATTTTTCAACAAATGGCGAGAAGTTGATATCATGCTCT
GAAGATGATCAAATTGTTTTGTATGACTGTGAAAAAGGCACTCAAACAAGAACTGTTAAT
TCAAAAAAATATGGAGTTGATTTAATTCATTTTACACATTCATCTATGACAGCAATTCAC
AGTTCAACGAAAGTAGATGACACAATAAGATATCTCAGTTTACACGATAACAAATATCTA
AGATATTTTCCTGGCCACACAAAGAAAGTTATTTCTCTCAATATTTCACCTATCGATGAT
ACCTTCATTTCTGGATCACTGGATAAAACTCTCAGATTATGGGATTTACGATCGCCAAAT
TGCCAAGGTGTAATGCATTTACAAGGGAAACCTGTTGCTGCATTTGATCCAGAAGGACTA
ATTTTTGCTGCTGGAGTTAATTCTGAATCAATTAAATTGTACGATTTAAGATCATATGAT
AAAGGACCATTTGTTACTTTTATGCTAAATCAAGAAAAAGAATGCGAGTGGACTGGATTA
AAATTTTCAAAAGATGGAAAGACAATTTTAATTAGCACAAATGGCTCAGTTATTCGTTTG
ATTGATGCATTTCACGGAACACCACTTCAAACTTTTACGGGTAAATTTGTGTACTATTCT
TTTATGAATATATCTATTTAAATAAAATTATATTGTTTTTAGGATATTTAAACAATAAAG
GAATACCAATTGAGGCGTCATTCAGTCCAGATTCACAATACATTTTTTCGGGTAGTACTG
ATGGACGTGTGCACGTGTGGAATGCAGATACTGGTTTTAAAGTTTGTGTTCTTAATGGTG
ATCATCCAAGTCCTGTACAATGTATTCAATTTAATCCGAAATACATGATGATGGTTTCAG
CATGTACTAATTTAGCTTTTTGGCTGCCGACTATTGAAGAAGAATAA
>g5882.t258 Gene=g5882 Length=246
MKLNDPVIRSFKVAKVFRENQDKLNSIDFSTNGEKLISCSEDDQIVLYDCEKGTQTRTVN
SKKYGVDLIHFTHSSMTAIHSSTKVDDTIRYLSLHDNKYLRYFPGHTKKVISLNISPIDD
TFISGSLDKTLRLWDLRSPNCQGVMHLQGKPVAAFDPEGLIFAAGVNSESIKLYDLRSYD
KGPFVTFMLNQEKECEWTGLKFSKDGKTILISTNGSVIRLIDAFHGTPLQTFTGKFVYYS
FMNISI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5882.t258 | Gene3D | G3DSA:2.130.10.10 | - | 2 | 246 | 0.0000e+00 |
| 3 | g5882.t258 | PANTHER | PTHR19861:SF0 | WD REPEAT-CONTAINING PROTEIN 82 | 2 | 235 | 0.0000e+00 |
| 4 | g5882.t258 | PANTHER | PTHR19861 | WD40 REPEAT PROTEIN SWD2 | 2 | 235 | 0.0000e+00 |
| 2 | g5882.t258 | Pfam | PF00400 | WD domain, G-beta repeat | 16 | 49 | 5.3000e-02 |
| 1 | g5882.t258 | Pfam | PF00400 | WD domain, G-beta repeat | 99 | 135 | 6.4000e-05 |
| 11 | g5882.t258 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 17 | 144 | 1.9802e+01 |
| 13 | g5882.t258 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 17 | 58 | 9.8070e+00 |
| 12 | g5882.t258 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 103 | 144 | 1.4719e+01 |
| 7 | g5882.t258 | SMART | SM00320 | WD40_4 | 10 | 49 | 1.8000e-04 |
| 8 | g5882.t258 | SMART | SM00320 | WD40_4 | 96 | 135 | 2.0000e-07 |
| 6 | g5882.t258 | SMART | SM00320 | WD40_4 | 138 | 175 | 5.0000e+01 |
| 9 | g5882.t258 | SMART | SM00320 | WD40_4 | 180 | 222 | 1.0000e+02 |
| 5 | g5882.t258 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 9 | 234 | 0.0000e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5882/g5882.t258; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5882.t258.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 transcript has been annotated with K14962 (COMPASS component SWD2)
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.
