General information for g5882.t260
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.t260 | TTS | g5882.t260 | 12573421 | 12573421 |
| chr_2 | g5882 | g5882.t260 | isoform | g5882.t260 | 12573531 | 12574934 |
| chr_2 | g5882 | g5882.t260 | exon | g5882.t260.exon1 | 12573531 | 12573775 |
| chr_2 | g5882 | g5882.t260 | cds | g5882.t260.CDS1 | 12573531 | 12573775 |
| chr_2 | g5882 | g5882.t260 | exon | g5882.t260.exon2 | 12573838 | 12574309 |
| chr_2 | g5882 | g5882.t260 | cds | g5882.t260.CDS2 | 12573838 | 12574309 |
| chr_2 | g5882 | g5882.t260 | exon | g5882.t260.exon3 | 12574384 | 12574740 |
| chr_2 | g5882 | g5882.t260 | cds | g5882.t260.CDS3 | 12574384 | 12574611 |
| chr_2 | g5882 | g5882.t260 | TSS | g5882.t260 | 12574711 | 12574711 |
| chr_2 | g5882 | g5882.t260 | exon | g5882.t260.exon4 | 12574803 | 12574934 |
Sequences
>g5882.t260 Gene=g5882 Length=1206
CTTAATTTCACTGGAATATTATATCTTATGCACTGATGAGGTAATATCTATTAATTTCAC
TGTTTTACTCACAGTATTTCAAGATTTATCCAAATGTTTTCAACAAAACAAGAATGGAGT
AAAATCACACATCATATTTTTAGGAGAACGACTTTGGTTTGTTTACAACAAAAAATAAAA
ATTTGACAAGTTCCGAAAACAAATTTATTAATTAAATCCCTGTAATTATTCATCAAAAAG
ATATTAAAAAAGTCTTTCAATATGAAGTTAAACGATCCAGTAATTCGTAGCTTTAAAGTG
GCAAAAGTATTTCGTGAAAATCAAGATAAATTAAATTCTATAGATTTTTCAACAAATGGC
GAGAAGTTGATATCATGCTCTGAAGATGATCAAATTGTTTTGTATGACTGTGAAAAAGGC
ACTCAAACAAGAACTGTTAATTCAAAAAAATATGGAGTTGATTTAATTCATTTTACACAT
TCATCTATGACAGCAATTCACAGTTCAACGAAAGTAGATGACACAATAAGATATCTCAGT
TTACACGATAACAAATATCTAAGATATTTTCCTGGCCACACAAAGAAAGTTATTTCTCTC
AATATTTCACCTATCGATGATACCTTCATTTCTGGATCACTGGATAAAACTCTCAGATTA
TGGGATTTACGATCGCCAAATTGCCAAGGTGTAATGCATTTACAAGGGAAACCTGTTGCT
GCATTTGATCCAGAAGGACTAATTTTTGCTGCTGGAGTTAATTCTGAATCAATTAAATTG
TACGATTTAAGATCATATGATAAAGGACCATTTGTTACTTTTATGCTAAATCAAGAAAAA
GAATGCGAGTGGACTGGATTAAAATTTTCAAAAGATGGAAAGACAATTTTAATTAGCACA
AATGGCTCAGTTATTCGTTTGATTGATGCATTTCACGGAACACCACTTCAAACTTTTACG
GGATATTTAAACAATAAAGGAATACCAATTGAGGCGTCATTCAGTCCAGATTCACAATAC
ATTTTTTCGGGTAGTACTGATGGACGTGTGCACGTGTGGAATGCAGATACTGGTTTTAAA
GTTTGTGTTCTTAATGGTGATCATCCAAGTCCTGTACAATGTATTCAATTTAATCCGAAA
TACATGATGATGGTTTCAGCATGTACTAATTTAGCTTTTTGGCTGCCGACTATTGAAGAA
GAATAA
>g5882.t260 Gene=g5882 Length=314
MKLNDPVIRSFKVAKVFRENQDKLNSIDFSTNGEKLISCSEDDQIVLYDCEKGTQTRTVN
SKKYGVDLIHFTHSSMTAIHSSTKVDDTIRYLSLHDNKYLRYFPGHTKKVISLNISPIDD
TFISGSLDKTLRLWDLRSPNCQGVMHLQGKPVAAFDPEGLIFAAGVNSESIKLYDLRSYD
KGPFVTFMLNQEKECEWTGLKFSKDGKTILISTNGSVIRLIDAFHGTPLQTFTGYLNNKG
IPIEASFSPDSQYIFSGSTDGRVHVWNADTGFKVCVLNGDHPSPVQCIQFNPKYMMMVSA
CTNLAFWLPTIEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5882.t260 | CDD | cd00200 | WD40 | 15 | 300 | 3.56541E-45 |
| 10 | g5882.t260 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 307 | 6.9E-58 |
| 4 | g5882.t260 | PANTHER | PTHR19861:SF0 | WD REPEAT-CONTAINING PROTEIN 82 | 2 | 313 | 1.9E-137 |
| 5 | g5882.t260 | PANTHER | PTHR19861 | WD40 REPEAT PROTEIN SWD2 | 2 | 313 | 1.9E-137 |
| 6 | g5882.t260 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 36 | 50 | 1.2E-5 |
| 8 | g5882.t260 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 122 | 136 | 1.2E-5 |
| 7 | g5882.t260 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 254 | 268 | 1.2E-5 |
| 3 | g5882.t260 | Pfam | PF00400 | WD domain, G-beta repeat | 16 | 49 | 0.075 |
| 2 | g5882.t260 | Pfam | PF00400 | WD domain, G-beta repeat | 99 | 135 | 9.2E-5 |
| 1 | g5882.t260 | Pfam | PF00400 | WD domain, G-beta repeat | 227 | 267 | 2.4E-5 |
| 12 | g5882.t260 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 254 | 268 | - |
| 19 | g5882.t260 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 17 | 314 | 26.577 |
| 21 | g5882.t260 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 17 | 58 | 9.807 |
| 20 | g5882.t260 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 103 | 144 | 14.719 |
| 22 | g5882.t260 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 246 | 271 | 10.909 |
| 14 | g5882.t260 | SMART | SM00320 | WD40_4 | 10 | 49 | 1.8E-4 |
| 15 | g5882.t260 | SMART | SM00320 | WD40_4 | 96 | 135 | 2.1E-7 |
| 13 | g5882.t260 | SMART | SM00320 | WD40_4 | 138 | 175 | 50.0 |
| 18 | g5882.t260 | SMART | SM00320 | WD40_4 | 180 | 222 | 100.0 |
| 17 | g5882.t260 | SMART | SM00320 | WD40_4 | 225 | 267 | 9.3E-4 |
| 16 | g5882.t260 | SMART | SM00320 | WD40_4 | 270 | 308 | 8.7 |
| 9 | g5882.t260 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 9 | 302 | 9.71E-59 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5882/g5882.t260; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5882.t260.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.
