Gene detail

Detailed information of acyt_s0033.g114.t1 in Acropora cytherea

Genomic Location: sc0000033_pilon:1562784...1575168
NR annotation: XP_029187349.2, DNA repair protein RAD51 homolog 2-like [Acropora millepora]
Species Acropora cytherea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

acyt_s0033.g114.t1

CATAGAAAATACAGCCCTGAGAAGCCCTAGATTCATATGTTACATGAAGTATGTGCCCCCTTCCTGCAATGTTTTGATCTTTCGCTATGCAGCCTCCCATCACAATAGCTCGGTTCCCAAGCACACCTGGATTTCAAAATGGCGATTCAGGCACTCTTTCACAGAACAAAATAGAATTGAATGAAATGCGCAAAACTGAGATCACTTCAGGCTCTCAATGAGTGGAAAGGAGAGTAACAATATGAATTTCCCTAATTTTCCGAAAAACACATGAAAATTATGTCCTCTCGAAAACTACGACGTGTCCATGGGTTGCGCTCTGAAATAGTGAACAAACTCGCTAAGGATGGGATACTAACCTGCAAGTTGATTCACACAGGATGTGCTTCAGAAAAATGTCCTGGAACTTCTCAAGTCAACTGGAGCAAATTACCAAGAGGTGTTAGCTATCCAGAAAGCTGTGAGTCAGTCTATTATTCCGAAAATGCAAACAGCTTATTCCTTATGGAAGGAGTCAGATCACCAGAAATCTTTCTTTCAAACAACACTTGTGGACCTTGATAAGCAGCTTCATGGTGGACTGAAATGTGGCACAATCACAGAGATTGCTGGACCGTCAGGTTGTGGCAAGACACAGTTTTGCATTATGCTTAGTGTATTGGCAGTCCTACCTCAAGGTGCTGGAGGATTGGATGCCAGTGTAATTTATATTGATACTGAAGCAGCATTCAGTGCAAAAAGGTTGGTAGAAGTCGCTTCTAATCGGTTCCCAGACCTTTTCAACTCAGAAGAGTCCTTGATTCAATTGTCCCAGCGAGTGTATGTTTATTGGGAATCAACGTGCAGCTCACTGTGGGAAAGGTTACAGAGACTTGAAGAAGATGTTATTTCAAAGCGTGTGAAACTCATTATCCTTGACTCTGTAGCTTCCCTTGTCAGAAAGGAGTTTGATAGCCGGGTGTCCAGGAACTTAAATGAAAGAACTGCCCTTCTTTCCAAAGAGGCGGTAATTCTAAAGTATCTTGCCGAGACCTTTCACATTCCGGTTGTCGTTACCAATCAAATCACCACCCGCTTTGTGGGAGAAGGGCCTGGTGTCGGAAATGTTTTTGATAAAACCCAGACTTTTCAGGACGCGGATGGCGGCGTGGGTGCTGAGCCGGAGGACGACGATGGAAGCCGGGTAACCGCTGCTTTGGGAAACACGTGGTCTCATGCAGTGAATACGCGTCTGATCGTACAATATTTGGATGAAAAGTTTCGTCAGATACTGGTTTCCAAATCACCAATAGCTCCGTTTGGGACTTTTATCTACACAATCCAAGCGGAAGGAATAGTTTTGGAAAGACAAAATTCTTTGCGCGAAGAGCTTGGTGGAAACCCTTCCCTTCAGAATATTCAAGTTCGTTCAGCATTTTGATAGTCACGTGACAACCGCCTACTTCGTAACCGAGGGAAAGTGCGCCCCACTCTCAATCGTGCGTCCAGGTTCCTTTCGCGCCAATTTTCCTTCCTAACCCTGCTGGCAGAGTCTCTCAAAAACTCGGGCTCTTCTGACAGGATACTGCCTCCCGTTCGCTTTAGAGCACCCTGCACGCATGCTAAGTGTAGATTGTAACGTCCTTTTGGGCAGCTTTTAATTTATTTATTGTTATGGTGTTAGTATCCGTACAACCTCTTGGTTTATCCCAAATTTAAGATTTCACTTGTACATTTGCATCCAGCCAAAGATGGTTTTGTGAACGTAAGGAGGTAACGATGAGCTAATTCTTCTTTACTGTTTTCTCCTCATAGTAACCTCTGGTGAAAAAGTGCAGTTGGCATTCTGACACATTTTTGCAATCATTACCTTTCGGTTTCCGTAAATTCGTTTCAATTCGTATCTTTCATAGCAACTGGAGATGAAGGCGCATTATTCGTTTGTTTGCAGAGTTTTCCTCATTAGGGCCCAAATCCCGGATCCCGTGGTTATTTGTGGTCCCGTCCCGCCATCACGTCCAAAGGAGCATTTTCATCTCGTATTTCTAAGTCTAtagggagtttaagatctacgacgcgacggcatcgaccccgtcacaagtttcgcatatttaatcaacaaaaacaaaagctttgcacgcccttcaagtgtttcttttaattctgtacatttctttcccgttctcggcaaatttgcaacgcgaaatgaccatttctcaagttttgcagagaacgtgaacacgcagccgccaatttgaattttcttttttagctttgacactgcacctctttagttagttcctgggtagttccgctagcttttcaaaagttaaacaaattggcataatattgaaaaaagaaaaggacaaacttgaacttgcaattttgagcgacgtttttgctaccgttgcgtcgtaggtcttaaattccctTATGATTCTCCAGCACACCGTCATATTAACTTTTGGACTACGTGCATGGCTTTGAAGTGCTGAAAGTGACACCCAATCGAAGAAATACCAAAGTCTATTTAAAAGCAAAATATTTTAGTTGTGAGGTTGGCTTGCAAAATTTGGGCTGAAAGGAAAATGAAGGTCAAGGAAATCACTATGACAGGGATATTATTTCAATGAATACCAATCTCAACAGGACCTATGCGACAAAAAAACAAGCCTCCTAACAAATGTAATTTGGGTTATAAGCGGCTCCAGGTCTTAATAAATTCACTGTTTTCTTCAATCTTGCGGTTCGGGTGCGGCGAAGTTGAACCTTCTTTTGTAATGTTGTTATTTCGGATTTGGGCAGATCAAGGTTTTGAAACAGCACAGATTTCACACTGTAACGATTAAAGCCCAGAAGAACTGAAGAAAGGTCACATGCCGTTGTTGGCGGATTTGCAAGAGATTGAGTGTATTAAAAAGATTTAAGAGGTTTTAAGGGGAGCGGAAATCAAGAGAAATGTCGAATGTGTCGAAACAGGAAAATGTTTGCGAAAGCTGTCAAAAAGCATTGACCCTTGGCAGAAAATCCAATTTCAGAGCCAAATGTATACATTGCAACTAAAATTCATTAAAAAGTTGCGAAAGAGTAGCAAGGACGAATGGATGGGACCCATGCGGTTGAGTTGGCGCCCTGCTGTCAAGCCATCAGCGTGGAGCCGCCGGTCAAACAGGATTTCGGTTTTTGCATCCTGTCAGAAATGAGATCATGTTGAACAATAAATTTTCCCTTACCCCTCCCCCCAACCCCCCGCTCATGGATTGCATATGAGAATGAATGGAAATGAGGAGGATAGTTGCCCTTTGGAAGCATGGGGATTACGTAAGTTCTTAACCCCTGGGGGTAGGACTCCGAAAAGACGCTCCACGATGAAGTGAGTCTCTTAAACTTTTTTTTTTCTCATTTTAAGCTGCCTTAAATCAGGCTAAAGAAGCAAGTGCCATTGCTTAACATCAGAGAACATTTGATAAACCCGAAAGTCATAAAAAGATGCGTGTGGGATAACCAGTATTGATGCTTGAAATCAAATGTACGGTGTTTACAAAAGTTATTAATGAAACAATTGTATTATC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O15315	DNA repair protein RAD51 homolog 2 OS=Homo sapiens OX=9606 GN=RAD51B PE=1 SV=2
O35719	DNA repair protein RAD51 homolog 2 OS=Mus musculus OX=10090 GN=Rad51b PE=2 SV=2
Q9V233	DNA repair and recombination protein RadA OS=Pyrococcus abyssi (strain GE5 / Orsay) OX=272844 GN=radA PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007425 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08423 all species →	Rad51	Rad51	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013632 all species →	Domain	DNA recombination and repair protein Rad51-like, C-terminal	Interproscan
IPR016467 all species →	Family	DNA recombination and repair protein, RecA-like	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR020588 all species →	Domain	DNA recombination and repair protein RecA-like, ATP-binding domain	Interproscan
IPR030548 all species →	Family	DNA repair protein RAD51 homologue 2	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46456 all species →	DNA REPAIR PROTEIN RAD51 HOMOLOG 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor activity	Interproscan
GO:0000400 all species →	Molecular Function	four-way junction DNA binding	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005657 all species →	Cellular Component	replication fork	Interproscan
GO:0008094 all species →	Molecular Function	ATP-dependent activity, acting on DNA	Interproscan
GO:0033063 all species →	Cellular Component	Rad51B-Rad51C-Rad51D-XRCC2 complex	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis 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
K10869	RAD51L1, RAD51B; RAD51-like protein 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 Acropora cytherea 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 Acropora cytherea, 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 →