Gene detail

Detailed information of XP_058944545.2 in Pocillopora verrucosa

Genomic Location: chr1:11801272...11808349
NR annotation: no NCBI-NR hit recorded
Species Pocillopora verrucosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_059088562.2

TTAGGTTGGTTCGCGCCAAAGTCACCAGCACATTGAACTATCTGCGAGTATTGTGGACGTCTTGTGCGATAAGACTAACTAAAGAATGAGCAAATTTAGGAAAGAAACAGAATCCAAGAACAAATGTGTGGAGCTTGTTGGATCAGAAGATCACACGCATGATTTCACTGTAGATGAAATCCAGCGAATTCGAGCTAATCTGCTGACATGGTACGACAAGAATTGCAGAAAGCTTCCCTGGAGAGAGTTGGCGTCTCAACCTGATCTAAATAGGCGTGCATATGCTGTGTGGGTCTCTGAAGTTATGCTGCAACAAACACAGGTCGCCACCGTAAAGGAGTATTACATTCGCTGGATGGAGAAATGGCCGACTGTTGAACATTTGTCGCGTGCGAGTTTGGAAGAAGTGAACGAGATGTGGTCAGGACTTGGTTACTATTCGCGAGCAAAGAGACTCCACGATGGAGCTAAAAAGGTTGtagagaaaatgaaaggaaacatACCTTCCACAGCATCTGAACTACTGAAAGAGCTACCAGGAGTTGGTAAATACACTGCAGGCGCTATTGCTTCCATTTCATTTGGTGAGTGCACTGGAATAGTTGATGGAAATGTGATTAGAGTTTTATCAAGGCTTTGTGGTATTGGTGCTGTAAGTTCCAGTACTCAAGCTGAGCGGAAGTTTTGGGAGCTTTCTCATAAACTTGTTCCTGAAGATAGACCTGGTGAGTTTAATCAGGCTTTAATGGAATTTGGAGCAACACTGTGTACACCTCAAGCTCCACGGTGTCATGTATGCCCTCTGCAAAGGGATTGTAGTGCTTTAAAGCAAGTAGTGAAACAGGACTCTCCAGTATCCATTCTGCATAGAGAAAAAGGACTAACATCCAGCAATGGCATAAAAGTTGATAAACATGTTGACATTGAAGAATGTATCCTTTGCCTACCATCTTCACTGTGGAAGCCCTCCCTCGGTGTTTGCAATTACCCACAGAAACCTAAACGGAAACAACCTAAGGAGGAGACTTTGgctgttgttgttattaaaCATGACATGGAGGTGGGATCTCATTTTCTGTTGACTCAGAGACCCAAAACAGGACTTTTAGCAGGCTTGTGGGATTTCCCTAATGTTGCTGTTGAATCAAATCAATCTGATGCTTACATGTTTACTACCCTTTGTAACTTCTTGGAAAACAACCTGGGTATCACCCTCAAACAGAGGACTCAAAAAAGAATAGCAGAGGTTTCTCATAAATTCTCGCACGTTCATCATAAGTACATGGTGTTTTCATATGAGCACCCTGAAATCAAGCATTTGCTTCAAACCTcccaagaaaaaagcaaaataaggTGGATAACAAGAGAAGACTTAGATACTGCAGCTCTTTCCACAGCCATGCGGAAAGTTTTCACTGCCTTCGAAATGCACAACAGTGGTGAGAATGAAAAACAAGCCAAAGTGgacaggaaaagaaagagaccAAATTCTCATGATGGCAGAAAACAGATGGTGCTTGATGGATTTCTCAAGTCAAAGGACCAACAAAATTCACCCATTGCAAGCATAAGAAAACCCTAAACAAAGATCATGTATTACAATGTGAGTAAAAAAGTGATGTACAAATGGAAAATGATATGATCTGGTTTGGCCAAGCAAAGGAAGGTTTGGATTGTGGCATCAAAATTTGTGAACTTGTACATATGGAAATTTGATACTAACAGGATACTATCTTGTATTAGTTTTGCAGACTTCTGCCATGTTTAATAAAGACCATGTGGTTAGAGTGAGATAAGACATATATAATGACATCTCCCCTCTAAACAACTATGCAGAGTAATATACAAGCAATTCAAATATCAATATTGTTCACAGTTCATTGTCCAAGAATTATgtaaaaataggtccgcaatgcgtatATGTGTGGCTTACAAAATTGAGCTGCTTCTTGGTGTCTGGTATCTCATTGGGTTTCAATTAGAAGAGCTACTATCTGATAACCattagatagttttcaatatcGATCCTGTTCATCAATAACACAGGATAAATAGCATACAAAAGTCCTGAAATGTTCATTCTGAAGATGAGAGTtattggccaaactttgttattggaggtctcattttgacaatAAAGGTTGTACATGTAACCCAAGGATTTTAGGAACtaaaaaaacatcagcataatctCCCATAGTGGTCTGATAGATTCAGTCATGATTATGTTTATGTAATGAAgtggaattgacttctgaagtttgtaggttgattgtcttttccaaggcaagtgatgtgaaatgaactctagggaagaatttcatatgaatatttttgacattttgtgtaccagtacacAAGGACAAAACTTTGCAGAAGGGCAGGGACATTTGGGAAATGATGCAATCTACACTAGAAGCCATTGGgagcttgatttggtttgaatttatgactaattttggacaatacatacatgtaaagtaacacaATGCTGAGTGTAGGTTTCTTTAGTCCATTAGGGCATAAAGTTCAACTTTCAGTGAGTTGAGAGCAAAAATTTTACTATAATCATtgtatttaggttttgtgggactgtattttcaataaagaacagaaaaatttagctCAGATAGGTAGATATGAGGTTGTAAATGGAAGAGTCTAGAGAAAAAAGATTGGTGCAATTACAAGATCAGaacacaagcaatattttaatgaatcataTGTTGAGTTAAGTACTCTGAAGTTACATTTCTAATATTTTTTAACCCAATAAGATTTATAATTTGACCTGgaggttttatttaacagaaagttcaatAGAGATAGAGTGTCACCATGATAGATTTCAGGAACAGTAATCAGAGACACAACTTAAACACAGCAGAGTTCAATGTACAGGCAAGTGCATGATGGTATCATATGATTTAAACTACCAGaaactttcaagttttcttattattgaaattgtaatttcatgccagtgagtctaccaaattcaagttatttGGAGAAATGAATAGGTGAACTTGATATCATCATGCAAATGGTCGACTTCGcatcatcatgcaaagtgctaatctaccgtacaaaaaggtccaaaacaaacatggcaagCAACTGAACTTCATGTATCACTCTGTGTTAGAGCCCACAAGAGGACTTGTGAGACTTGCTTCACTCTCATTTGCCAGAACAAGATTAAACTTCTGGTAacaatcaaaattcagaatgactgTGACAGTTATGGAACTGATCTGTTAAGACTGTGCTTTTAAGGGGTCTACAGATATGATTAGAACCCCTGGGTCTCCAAGGATACCTGATGGTTATCTAATGTGTGTGCagtttaaagtatttaaaaaattttcaagtgctCATCATATGAGAAATCATGctattaattattcataatgtaTATATGAAAGATACACATTTTcaggaaatcaacaaactgatggcagataaatttgacagtattgactaaatgaagtttgccatcaaaatttgtccttcagctGAATTCTTACTCAGGAAAGCAATTTTGTTAGTGTTTATCAATATACATAAAAGTATCTCAgcttttgtatatttttgtcagctactgcatgtatcaatcagaacaaactactttgtgtaaatctgattaGTTTTTAATGTGATCTCTTATTGCTGAGcctagtttatattattttgtacatgAGTTATTACTTCTTCactaatgataaatgaaaaaggcacctagttattttcagccaatcaaaaaagtgtaatttttcatgtatgtcAGTACTGTGATGAATTTACCAAACCAAACAAGTAACTGGAAAGGAGTTGTAGTCTATCAAATAAAGGCCTAATACACATGTATTGCTACCAAGTATAGATACCAATGCTTATCTGAACCATTATGAAGAGAATCTAGAAGACTGTTAAGCTTGAAGGAAGTCATGAAATGTTAAGGTCTGAATAATTCTGGCcataacttggaaaacataacACTAATCACATTTCAGTTAACATTAAAGCACTAGGCTCCTATTCATTTAGTCCTATTCATAAGTTTCAATGTGGCACAACCTGCACTAAAGGTCCAGACCATGAAATGTTGGCCTGTGAGAGCACAACTCCATGCTGTAATCTGCACTTAGAAGACAAGCCAACTATAGGAAAGCCAGCATGTGAAATCTAAGAAACAAAGATGAACgaaaaactagataaaaaacCGATCTTCGACAGCGTGTTACAGCCACCATTGCAAAATGGTCACTTTCTGAAGCTTTGAAGCTCAGGTAACTTAGCCAAGCATAGACTGGAACCTATCTTCGACGATAgtaaaccacgtgacaagcgcTCTGTTCACCATGACAAATCCAGCCAGGAATAAATATCTTCAATCATGACATAGTGTGGTTTACACTTCgtgtaagccacacaaaaatCGTTTTAAAGTTAGTGTTCTCAGCTGACAACAACAACTCAGCAACTCAGCCTAGCATTTTTTCAACAATTATCAGTCATACCAGTAATATACCAAGTCATCTTGTCTTGGTACCCAAATAGTATGGCCAGATCTTGTTCTGACTACTTGAGGGGTCTTGACGATGTTTCTGTCACTCCCTGTGCTCTTGGTGATTTCTCTGTCACCTTTTGCACTTGCGATGGTGCCTTTGTTAACTTATGAAGTCTTGATGTTCTCTCTCCTGTTTCGTCTGTAGAGAGTTCCACCGCAGATCAGAATTACTGATCAAGGGGTGCGAGCAAGTTTTGTAACTTTGGAAggttttttgccattttttgtttatattcGAACAGCATCACTAGTTTTTGCAG

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005361 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00730 all species →	HhH-GPD	HhH-GPD superfamily base excision DNA repair protein	Domain	Interproscan
PF14815 all species →	NUDIX_4	NUDIX domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004036 all species →	Conserved_site	Endonuclease III-like, conserved site-2	Interproscan
IPR003265 all species →	Domain	HhH-GPD domain	Interproscan
IPR000086 all species →	Domain	NUDIX hydrolase domain	Interproscan
IPR015797 all species →	Homologous_superfamily	NUDIX hydrolase-like domain superfamily	Interproscan
IPR023170 all species →	Homologous_superfamily	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Interproscan
IPR044298 all species →	Family	Adenine/Thymine-DNA glycosylase	Interproscan
IPR029119 all species →	Domain	Adenine DNA glycosylase, C-terminal	Interproscan
IPR011257 all species →	Homologous_superfamily	DNA glycosylase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42944 all species →	ADENINE DNA GLYCOSYLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0000701 all species →	Molecular Function	purine-specific mismatch base pair DNA N-glycosylase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0016798 all species →	Molecular Function	hydrolase activity, acting on glycosyl bonds	Interproscan
GO:0032357 all species →	Molecular Function	oxidized purine DNA binding	Interproscan
GO:0034039 all species →	Molecular Function	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity	Interproscan
GO:0035485 all species →	Molecular Function	adenine/guanine mispair binding	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K03575	mutY; A/G-specific adenine glycosylase	EC:3.2.2.31	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Pocillopora verrucosa tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Pocillopora verrucosa, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →