Gene detail

Detailed information of BRAKERYMEP00000030088.1 in Astreopora myriophthalma

Genomic Location: BLFK01000871.1:2373353...2380465
NR annotation: XP_029208805.2, flap endonuclease GEN homolog 1-like [Acropora millepora]
Species Astreopora myriophthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERYMET00000030088

ATGGGTGTAAACCAACTTTGGAACATACTGGAGCCAGTCAAGAGAAGGGAAAACCTGTCTGCGCTTCGCAATAAGACGCTGTGTGTAGATTTGAGTTGCTGGATTTGCGAGGCGCGCTGTGCAAAAGGACTAAAGCAAAATGTAAGCAAACCGCATCTCAGGAATCTTTTTTTCCGATTGCTTCATTTGACGCGACTCGGAGTCAAGCTGGTATTTGTTGTGGATGGGGCACCACCCGAACTGAAATGGGAAGCCATAGCGAAAAGAATTCAGGCGAGAAGTGGCGGGCAATATTGGAGTTCGAAGAATTCCAAGAAAACTCTCTCGGGTGCGCGCGTTGGGCGATCACACTTTGCTGTATGGGTAAGAGAGTGCCGTGAGCTCTTGGACCTTTTGGGGTTGCCCTGTATTGAGAGCAAAGGTGAAGCAGAAGCTCTTTGTGCCTGGCTTGATCTCCATCAGATTGTGGATGGCTGCATAACAAATGATGGCGATGCATTTCTGTATGGAGCAAGAACTGTTTACAAAGATCTTTGTATCAGTGGGAAGGATGCATCAGTGGAATGCTACAAAATGGCAGATGTAGAGACTCAGCTCAATCTCAACAGGCAGATGCTGGTGGCTCTTGCAGTACTTCTCGGCTGTGATTACCTTCCTCAAGGAGTGTCAGGAGTTGGAAAAGAAATTGCCATGAAGTTGATCAGGGCTGTCAATCACAACAATTTAATTGACAGGTTTTATGAATGGACAAAAAGTACATGCAAGGATGAAGACCTTCCAAGTGTGGAGAAATCTGTTAAATGCAAAGCCCTTAAAGACAAGAACTTTCCTCATCATAAGGTTATACAAGAATTTTTGGCTCCTAAAGTGGTCCCTCAGCAAATTTCTCTCAAGATTGTGAGTCCAGAACTGGGGGGACTGCAGGTTCTTCCACTGATCACTTACTGGCAAATGACAACATCACTGGATCATCACCCAGTAACACTGGTTCAACCGTGTAGAATAGTGAAAGCTCGAATCCAGCAGAAAGTGGAATGTTATGAAGTCGAGTGGCAAAATGTGGAATTGGGTGAAACATGTCCTAATTCTTTTATTACTGTTGAAACCAGAGAGCTTTTTAATCAGGCTTATCCTGACATTGTGGACGAATTCAATAACACAGTGAAAGCAAAACTGTTGAAAAAGCCAAAGAGGAAGCGAGAAGAAAAGGTTTCAATATCCCATGGCTGTGAAACTGAAATTGACTTACTATCCAAGCAGCTGAAAGATTTAAGTGTGGATCAACTGTCTGAACATTGCTATGCATCTGCCACTCTGGATGAAAAGGAATATGTAGCAGCTGATGACAAGATCTCTGATGAAGAATCATTGCAGGACATCATTGACTCAATACTACCATCCAGCAGTGACAATCATTGGTGTTCCACAGAGAGTTGTGGTTCCTTAACAAGAATGAAAGATGGGAGTGGCAATTTATTTGCCGTGGGTATAACTTGCACACACGGTGGtgacaataatgatgacaatgataataataaaggTTCTGATGAAACCGCTAGGGATGGCTTTCTACATGTTTTCAAGCCTTTGCAGGTGAAAGTTAAGCAAGCCACACACGAACATAATCCATTGTGCAAGTCGACTGCTCAAAACCATAATTGTCCTTACTCAGAGGACTGTAAGATTTTGCAGTTAAAATCTGCCAAAGGTAATCCGCATCTTTTGGACCAGAATCATAAAAAAGGAGATAAGCAGTTTGGGATTTATCGTGAAGAGCCAGTTATATCATGCAGAACACAGAAAGCTGAGTGGAAACAAATCTCATGCTGTAAAAATGTAATTGTCATTGATTCAAGTGATGAAGATGATTCTCCCAGGGAGTGTATTTTcaagcaaagtttaaaaacaccAGCAGCAAAAGACCTTCCTAATCATGATGACCTAAAAGAGATCTTTGGGTCCAGTGACCTTTGGTCcagtgataatgatgatgaagtgTCAAACAGCCCTGATGGTGGTAAAGCTTCCTTACCTATGTATTCCTCTATACAGACTGCAGATTCTTCTGGGACTGATTACGCacagaaaacaatgcaaaatggAAATGCACATTTCTCTTGTGACACAGATTTCACTGATTTCACAAACCCAGAGTTGGATGAAAATTGTGGTGAAAAGGGAGTACAAGGTTGCATCTCAAATGACTTACAAGATGTCTCCTGTATGAAATTGAATACCATTCCATGTAAGGAAGAACATCACTCCAGAAAAAGGAGCAACACAAGTGAGGTGCCAGCAAGAACAAGAAACCATGAAATGTTGCACAAATCAATTGTACAGGATTTTCAAAAGACCCTACAATGTGACACATGTAGTATGAACGATGCTAACAGTCCAGGGAACCCTGAAATGCTGCAAAAACAAGAACTGACGAAAGGAAGCATTGATTCTTCATTTGATAGTGATGATGAGGACCTCTCTGTCCCACTGGTTGACAGAATTAGGAGGAATATCAGGACAAAGCAAAGGCTTGCTAGTCTAGGGGTCATTTCTACCTCAAAAggttaa

Transcript

BRAKERYMET00000030088

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q17RS7	Flap endonuclease GEN homolog 1 OS=Homo sapiens OX=9606 GN=GEN1 PE=1 SV=2
Q8BMI4	Flap endonuclease GEN homolog 1 OS=Mus musculus OX=10090 GN=Gen1 PE=1 SV=2
Q8W5R1	Single-strand DNA endonuclease 1 OS=Oryza sativa subsp. japonica OX=39947 GN=SEND1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002386 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18704 all species →	Chromo_2	Chromatin organization modifier domain 2	Domain	Interproscan
PF00752 all species →	XPG_N	XPG N-terminal domain	Family	Interproscan
PF00867 all species →	XPG_I	XPG I-region	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR041012 all species →	Domain	Flap endonuclease GEN, chromatin organization modifier domain	Interproscan
IPR006085 all species →	Domain	XPG, N-terminal	Interproscan
IPR006086 all species →	Domain	XPG-I domain	Interproscan
IPR006084 all species →	Family	XPG/Rad2 endonuclease	Interproscan
IPR036279 all species →	Homologous_superfamily	5'-3' exonuclease, C-terminal domain superfamily	Interproscan
IPR029060 all species →	Homologous_superfamily	PIN-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11081 all species →	FLAP ENDONUCLEASE FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004518 all species →	Molecular Function	nuclease activity	Interproscan
GO:0000400 all species →	Molecular Function	four-way junction DNA binding	Interproscan
GO:0017108 all species →	Molecular Function	5'-flap endonuclease 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
K15338	GEN1, YEN1; holliday junction resolvase GEN1/YEN1	EC:3.1.-.-	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 Astreopora myriophthalma 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 Astreopora myriophthalma, 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 →