Gene loci information

Transcript annotation

  • This transcript has been annotated as WD repeat-containing protein 82.

Parent gene

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.t259 TTS g5882.t259 12572810 12572810
chr_2 g5882 g5882.t259 isoform g5882.t259 12573531 12574611
chr_2 g5882 g5882.t259 exon g5882.t259.exon1 12573531 12573775
chr_2 g5882 g5882.t259 cds g5882.t259.CDS1 12573531 12573775
chr_2 g5882 g5882.t259 exon g5882.t259.exon2 12573838 12574187
chr_2 g5882 g5882.t259 cds g5882.t259.CDS2 12573838 12574105
chr_2 g5882 g5882.t259 exon g5882.t259.exon3 12574241 12574309
chr_2 g5882 g5882.t259 exon g5882.t259.exon4 12574384 12574611
chr_2 g5882 g5882.t259 TSS g5882.t259 12574711 12574711

Sequences

>g5882.t259 Gene=g5882 Length=892
ATGAAGTTAAACGATCCAGTAATTCGTAGCTTTAAAGTGGCAAAAGTATTTCGTGAAAAT
CAAGATAAATTAAATTCTATAGATTTTTCAACAAATGGCGAGAAGTTGATATCATGCTCT
GAAGATGATCAAATTGTTTTGTATGACTGTGAAAAAGGCACTCAAACAAGAACTGTTAAT
TCAAAAAAATATGGAGTTGATTTAATTCATTTTACACATTCATCTATGACAGCAATTCAC
AGTTCAACGAAAGTAGATGACACAATAAGATATCTCAGTTTACACGATAACAAATATTAT
CGATGATACCTTCATTTCTGGATCACTGGATAAAACTCTCAGATTATGGGATTTACGATC
GCCAAATTGCCAAGGTGTAATGCATTTACAAGGGAAACCTGTTGCTGCATTTGATCCAGA
AGGACTAATTTTTGCTGCTGGAGTTAATTCTGAATCAATTAAATTGTACGATTTAAGATC
ATATGATAAAGGACCATTTGTTACTTTTATGCTAAATCAAGAAAAAGAATGCGAGTGGAC
TGGATTAAAATTTTCAAAAGATGGAAAGACAATTTTAATTAGCACAAATGGCTCAGTTAT
TCGTTTGATTGATGCATTTCACGGAACACCACTTCAAACTTTTACGGGATATTTAAACAA
TAAAGGAATACCAATTGAGGCGTCATTCAGTCCAGATTCACAATACATTTTTTCGGGTAG
TACTGATGGACGTGTGCACGTGTGGAATGCAGATACTGGTTTTAAAGTTTGTGTTCTTAA
TGGTGATCATCCAAGTCCTGTACAATGTATTCAATTTAATCCGAAATACATGATGATGGT
TTCAGCATGTACTAATTTAGCTTTTTGGCTGCCGACTATTGAAGAAGAATAA

>g5882.t259 Gene=g5882 Length=170
MHLQGKPVAAFDPEGLIFAAGVNSESIKLYDLRSYDKGPFVTFMLNQEKECEWTGLKFSK
DGKTILISTNGSVIRLIDAFHGTPLQTFTGYLNNKGIPIEASFSPDSQYIFSGSTDGRVH
VWNADTGFKVCVLNGDHPSPVQCIQFNPKYMMMVSACTNLAFWLPTIEEE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5882.t259 Gene3D G3DSA:2.130.10.10 - 5 164 5.9E-26
2 g5882.t259 PANTHER PTHR19861:SF0 WD REPEAT-CONTAINING PROTEIN 82 1 169 9.0E-67
3 g5882.t259 PANTHER PTHR19861 WD40 REPEAT PROTEIN SWD2 1 169 9.0E-67
1 g5882.t259 Pfam PF00400 WD domain, G-beta repeat 82 123 9.0E-6
8 g5882.t259 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 110 124 -
10 g5882.t259 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 1 170 13.448
11 g5882.t259 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 102 127 10.909
7 g5882.t259 SMART SM00320 WD40_4 36 78 100.0
6 g5882.t259 SMART SM00320 WD40_4 81 123 9.3E-4
5 g5882.t259 SMART SM00320 WD40_4 126 164 8.7
4 g5882.t259 SUPERFAMILY SSF50978 WD40 repeat-like 10 161 2.18E-29

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5882/g5882.t259; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5882.t259.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.

Raw TPM values