Gene detail

Detailed information of ENSCIQP00000009393.1 in Millepora alcicornis

Genomic Location: chr2:9912558...10048965
NR annotation: AKQ00060.1, apurinic/apyrimidinic endonuclease 1 [Hydra vulgaris]
Species Millepora alcicornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSCIQT00000011032

TTTAGagaaaagtaaatacaaattggtcATTGGAGAGTCAATAGTCTTTTAGCTGACATGGGTAAAAGGAAGAGCACAGAAAGAGGTGCGAAAACAAAGAAGACCAAAGAGTCAAAGTTAGAGAATGGTGAGGAAAGTTCAGAAGAAGTACAGATAGAGgAAAAGATTGAAAGTTATGACATTCTAACGAAAACCAAAAACGGCAgGACCCCAAATATTAAGATCTGCTCATGGAATGTTGCTGGGTTAAGAGCATGGGTGAAAAAAGGTggtcataaatatttgaaagatgagAATCCTGATATCGTTTGTTTGCAGGAAACCAAGTGCATGGAAAACGAACTACCAAGAGAGATTGATCATTACAAAGCAGGCAAGACTTTATTAGGTGAGAATAAAAATGGCTATCACATGTTTTGGTGCAATGGCGTGAAAAAAGGCTACAGTGGAGTCACGTTATGGTCGAAAAAGAAGCCATTGAAGGTTACATATGGAATGGATGTGCCAGAGCATGACAACGAAGGAAGACTGATCACAGCTGAATATGAGAAGTTTTACCTAATAACATCATaTGTTCCCAATTCAGGCAACAAATTAGTAAGACTGGATTACCGGCGAACTTGGAATACGTCTTTAAAAGATTATATAAACAATCTCAATAGCAAGAAACCAGTTGTATTTTGTGGGGACTTGAATGTGTCGCATAATGAAATAGATCTAGCAAATCCAAAGAGTAACAAAAGAAATGCTGGCTTTACGGATGAAGAACGGGAAGATTTCAGTGCACTTTTGGCAGATGGCTACATTGATTCTTTTCGCCACCTCTATCCTGAGAAAACTGGTGCATACACTTACTGGACGTTCATGGGTAATGCGAGAGCCAGAAATGTTGGTTGgCGATTGGATTATTTTGTGATTTCAAAAGCACTGGAAGCTTCACTTTGCGACAATGTGATACGATCTTCGATCAAAGGTAGCGACCACTGCCCAATAGTTTTAACACTAGCCTTTTAAAACAAGGAAATATTTGTGTAGAGAAAGGATTGGAGGAATCACGTCTTTGGATAAGATGATGGGACGTTGATAATCAAGCTGTCATAGTTTAGTATGACACAACGAATGAAAAACGAGAAacttaaaaacatgaaagaaagaaaaagaaaatatttgttagatAGTTATCAGGAGaagtatttttattgaaacatgTTATTTTTAGATGTACGTGTGAAAGACCTTGAGAAAtagtaaattataaaatattgagcaaaaatattaaacattgcCGTGAAAATTAGCCCAAGCGCTGCATCATAATTCTGGAGGATCATCTAGGACAACAAGATTCTATGTTTTCAGAGAAAGTGTACTTTCTCATTACCTCGGCAAAGTTTTTTGATGCGGAAGTATGGTATGCGAGATTTTAACTATCGAGATCCGTAATGTATCTGGAGATTGTTTTCTATGGGCGTTACCAACCGTTATAAATAAGCTAGATTCAAGGTTCAATCAAATCTTCAGTTTTCTTAACATAGTTCAAATTTGAACCAACAACACTCAGATTAAAATTTTCAGTGGATTTAtgtttaattgtatatttttatcaaCGTCTGACTTAAGTACAGAGGAACTGGAAACCGAAGCCAGTCTCGGTCCGAAACAGAATGCTCCCTTGAGAATGATAAAATAGTCTCTTGTACCCTTTTTTGTGTTGCTAAAGCAATGggaattgtattttttaatgttaacttgtTGGGGTTTGTTGTTTTTCTCAAGATTATTTAGACACGATGTCATCTTTTCTGGGTTCCAGATAACATATTTTGGGGTAGGTGGGTTTGCattaaaaattccttttataaATCTTGTAACTGTATCATTTTGTTCAATTGGCTTACCAGCACTGTTCATCACGGGAGATACATTTCTTACGGTGTTACGCAGTGCTCTgtattttcatcatgtttttgtttttccaatcaGAGTTTCAAACCATTTTGAGATGGATTAAGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A0MTA1	DNA repair nuclease APEX1 OS=Danio rerio OX=7955 GN=apex1 PE=1 SV=1
P28352	DNA repair nuclease/redox regulator APEX1 OS=Mus musculus OX=10090 GN=Apex1 PE=1 SV=2
P43138	DNA repair nuclease/redox regulator APEX1 OS=Rattus norvegicus OX=10116 GN=Apex1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003223 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03372 all species →	Exo_endo_phos	Endonuclease/Exonuclease/phosphatase family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020848 all species →	Conserved_site	AP endonuclease 1, conserved site	Interproscan
IPR036691 all species →	Homologous_superfamily	Endonuclease/exonuclease/phosphatase superfamily	Interproscan
IPR020847 all species →	Binding_site	AP endonuclease 1, binding site	Interproscan
IPR004808 all species →	Family	AP endonuclease 1	Interproscan
IPR005135 all species →	Domain	Endonuclease/exonuclease/phosphatase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22748 all species →	AP ENDONUCLEASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0004519 all species →	Molecular Function	endonuclease activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0003906 all species →	Molecular Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	Interproscan
GO:0004518 all species →	Molecular Function	nuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0008081 all species →	Molecular Function	phosphoric diester hydrolase activity	Interproscan
GO:0008311 all species →	Molecular Function	double-stranded DNA 3'-5' DNA exonuclease activity	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	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
K10771	APEX1; AP endonuclease 1	EC:3.1.11.2	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 Millepora alcicornis 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 Millepora alcicornis, 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 →