General information for g5882.t246
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t246 | TTS | g5882.t246 | 12572810 | 12572810 |
| chr_2 | g5882 | g5882.t246 | isoform | g5882.t246 | 12572884 | 12574384 |
| chr_2 | g5882 | g5882.t246 | exon | g5882.t246.exon1 | 12572884 | 12572927 |
| chr_2 | g5882 | g5882.t246 | exon | g5882.t246.exon2 | 12572980 | 12573110 |
| chr_2 | g5882 | g5882.t246 | exon | g5882.t246.exon3 | 12573181 | 12573280 |
| chr_2 | g5882 | g5882.t246 | exon | g5882.t246.exon4 | 12573370 | 12574384 |
| chr_2 | g5882 | g5882.t246 | cds | g5882.t246.CDS1 | 12573797 | 12574105 |
| chr_2 | g5882 | g5882.t246 | TSS | g5882.t246 | 12574711 | 12574711 |
Sequences
>g5882.t246 Gene=g5882 Length=1290
GGTTAGTTTTTTTCACTCATTCATAATTCACAGCATTTAGTATTTATTTTATTAATTTCT
TATGTATATTTATAGACAGCAATTCACAGTTCAACGAAAGTAGATGACACAATAAGATAT
CTCAGTTTACACGATAACAAATATCTAAGATATTTTCCTGGCCACACAAAGAAAGTTATT
TCTCTCAATATTTCACCTATCGATGATACCTTCATTTCTGGATCACTGGATAAAACTCTC
AGATTATGGGATTTACGATCGCCAAATTGCCAAGGTGTAATGCATTTACAAGGGAAACCT
GTTGCTGCATTTGATCCAGAAGGACTAATTTTTGCTGCTGGAGTTAATTCTGAATCAATT
AAATTGTACGATTTAAGATCATATGATAAAGGACCATTTGTTACTTTTATGCTAAATCAA
GAAAAAGAATGCGAGTGGACTGGATTAAAATTTTCAAAAGATGGAAAGACAATTTTAATT
AGCACAAATGGCTCAGTTATTCGTTTGATTGATGCATTTCACGGAACACCACTTCAAACT
TTTACGGGTAAATTTGTGTACTATTCTTTTATGAATATATCTATTTAAATAAAATTATAT
TGTTTTTAGGATATTTAAACAATAAAGGAATACCAATTGAGGCGTCATTCAGTCCAGATT
CACAATACATTTTTTCGGGTAGTACTGATGGACGTGTGCACGTGTGGAATGCAGATACTG
GTTTTAAAGTTTGTGTTCTTAATGGTGATCATCCAAGTCCTGTACAATGTATTCAATTTA
ATCCGAAATACATGATGATGGTTTCAGCATGTACTAATTTAGCTTTTTGGCTGCCGACTA
TTGAAGAAGAATAACATGATGAGTTTTAAATTTTATTGAGACTCTTTTTTACTCTGTCAT
TTACAAAGTTTTTTTAAATAAATGATTAAATAAAATATGTAAGCAATGTAAAATGCTGTA
TTTTCCAAGTTGTTGAATTAATTACTCGACTTTTTTCTTCTCATGAATCTGAACTTGGAT
AAAATTTTCCCAAGCACGCTCATAGATTGATACAATTCCTTCATAAATTGAATTGTCAGC
AACATCCTTAAACTTTCCTTCGACAAAATACTTCACTTACTTGTTGTTTTGTGTTATAAA
TTTCCAGTATTTCCCAACTTGCACCTTCAAGTTTATCAATATGCTTCTTCAAAAGACCAA
CAATATGCTCATGCTTTGATTGATCCTCAATATTCGAAACACCACCACAAAGTTGTTTAT
CTTGATCCATTTTTAATTTTCTAATGTTTC
>g5882.t246 Gene=g5882 Length=102
MHLQGKPVAAFDPEGLIFAAGVNSESIKLYDLRSYDKGPFVTFMLNQEKECEWTGLKFSK
DGKTILISTNGSVIRLIDAFHGTPLQTFTGKFVYYSFMNISI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5882.t246 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 102 | 0 |
| 1 | g5882.t246 | PANTHER | PTHR19861:SF0 | WD REPEAT-CONTAINING PROTEIN 82 | 1 | 91 | 0 |
| 2 | g5882.t246 | PANTHER | PTHR19861 | WD40 REPEAT PROTEIN SWD2 | 1 | 91 | 0 |
| 3 | g5882.t246 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 10 | 90 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5882/g5882.t246; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5882.t246.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.
