Gene detail

Detailed information of ENSOJPP00000012310.1 in Anthopleura xanthogrammica

Genomic Location: chr10:10993502...11006011
NR annotation: XP_031562883.1, LOW QUALITY PROTEIN: DNA repair and recombination protein RAD54-like [Actinia tenebrosa]
Species Anthopleura xanthogrammica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSOJPT00000014183

ATGCGAAGATCGAGTGCACCAAGCCAGCTCCTGAAGAGAAAGCAGCTTGATAACGAGGACAATGATGGAAGAAGACCAAAACAGaaaatgaaacttgATGCTGAACCTCCTTCCAGCCAGTACATCTCGCCCTTCAGAAAACCTCTGAAACCTCTAACAGATGTGACCAATGGCTGTTCATCTTCACTGTCAGCCCATGAGGCTATTATTCGCAACATTCTCTCCAAGCCTTTCAAAATTCCAATGTCAAACTATCAAGGACTTTCCTCAACTCGTGGTCTTGGAATCAGAAGAAAGGGTCCAAGAAGGTCCCTACATGATCCATATGAAGAAGACGCCCTTGTACTGTATGAGCCTCCTGTACTATCAGCACATGATCAATTAGCCGTAGATCTagaaaaacaagaagTACATGttgtgGTTGATCCATTGTTAGGAAACAAGTTAAGACCTCATCAGAGAGAGGGTGTCAAGTTCTTGTATGACTGTGTCACTGGAAATAAGATAGAAGGGAGTTATGGATGCATTATGGCTGATGAAATGGGGCTCGGTAAAACTTTACAGTGTATTGCCCTCATCTGGACTTTACTGCGTCAAGGACCAACAGGTCAACCCATTATAAACAAAGTTGTCATCGTTGCTCCATCAAGTTTAGTTAAAAACTGGTATAATGAACTGAACAAGTGGCTGGGAAGTAGAATCAATGCTGTAGCTATTGACTCAGGCAGCAAAGATGGAATAGACAAACAACTAGTTACTTACATGAGTCAACAAGGCAGTCGTACTCCCACCCCTGTACTGATTATCTCGTACGAGACATTCCGTCTACATGCAGCAGAGCTACACAAGGGCAGTGTTGGGCTGGTCATCTGTGATGAGGGTCACAGGCTGAAGAACCTGGAAAGTCAGACTTACCAAGCATTGAACAAACTGAATACCACTAAGCGTGTTCTTCTTTCAGGTACTCCAATCCAAAACGACTTGCTGGAATATTTTAGCTTGGTACACTTTGTTAATGAAGGAATTTTAGGTTCAGTATcagaattcaaaagaaaatttgagaTTCCAATCTTGAGAGGCAGAGATGCCGATGCGTCAGATAAGGACCATAAAACAGGAACTGAAAAACTGAATGAGCTTATTCTGCTagtaaataaatgtattataaGAAGAACAGCATCAATTCTGTCAAAATATCTACCAATCAAGGTGGAACAAGTGGTATGTTGTCACCTCACTCACCTTCAAACCCAGCTTTACAAACATTTAGTCCAGTCAAACGTGGCGCAACGGCTACAGAAAGTAGAATCAAAGAGTGGCGGTGTGTCTGCTTCTTCACTGGGTTTTATCACTAATCTCAAGAAACTGTGCAATCATCCAGAACTTATCTTTGAGAAGGCAAAGTTGCAGGAAGAGGGCTTTAGAGGTGCTTTACAGATCTTTCCCAATGGATTTTCTGACAAGCAAAATTTACTTCCTGATTTATCAgGTAAAATGCAAGTACTTGACTACATTCTGGCCATGACTAAATCAACTACAGATGACAAAGTTGTGTTGGTATCAAACTACACTCAAACACTGGACATCTTTGAAAAGCTCTGCAGACAAAGAAActATCAGTACGTTCGTCTTGATGGTAGTATGTCAATCAAGAAAAGACAGAAGATAGTAGACAAGTTCAATGATCCTAAGGGTGgtgatttcattttcatgcTCAGTAGTAAAGCAGGAGGCTGCGGCCTGAACCTGATTGGTGCAAACAGACTAGTGATGTTTGATCCTGACTGGAATCCTGCCAATGATGACCAGGCCATGGCTAGAGTATGGAGAGATGGTCAGAAGAAAAAGgtATTCATATACAGGCTTCTATCAACTGGAACCATAGAAGAAAAGATCTTCCAACGTCAAGCCCACAAGAAGGCTCTTAGCAGCTGTGTAGTAGATGAAGAGGAAGATGTTGAGAAACACTTCTCACTTGAACAGCTGAGAGATTTATTTCGCTTGAATGAAGATACCCTGAGTGATACTCATGACAAGTTCAAGTGTCGTCGATGTGTGAACAACATTCAGGTACAACCCCCCTCCGAGGACAAGAACTGCAGTGCAAGTCTCGCCCAATGGAACCATTCTGCAAGTAGTAAAAACCTAGAAGatattatattaaaacaaGCCTGGAAGTGTGGAGTCAGTTTTGTATTCCATCAAAAATCCCATGACAAACAACTTGGAGTATCTATTAGATAG

Transcript

ENSOJPT00000014183

gttgctgttgtttcgTATTTGTCAGAGTTTGGTGCTGAAACTGCACCAGAAATGACTTCTTTCCTGACTACAAGCCTTCTTTCTTGACCATTCTAGATCATTAAGCTTATAAGCAACATGCGAAGATCGAGTGCACCAAGCCAGCTCCTGAAGAGAAAGCAGCTTGATAACGAGGACAATGATGGAAGAAGACCAAAACAGaaaatgaaacttgATGCTGAACCTCCTTCCAGCCAGTACATCTCGCCCTTCAGAAAACCTCTGAAACCTCTAACAGATGTGACCAATGGCTGTTCATCTTCACTGTCAGCCCATGAGGCTATTATTCGCAACATTCTCTCCAAGCCTTTCAAAATTCCAATGTCAAACTATCAAGGACTTTCCTCAACTCGTGGTCTTGGAATCAGAAGAAAGGGTCCAAGAAGGTCCCTACATGATCCATATGAAGAAGACGCCCTTGTACTGTATGAGCCTCCTGTACTATCAGCACATGATCAATTAGCCGTAGATCTagaaaaacaagaagTACATGttgtgGTTGATCCATTGTTAGGAAACAAGTTAAGACCTCATCAGAGAGAGGGTGTCAAGTTCTTGTATGACTGTGTCACTGGAAATAAGATAGAAGGGAGTTATGGATGCATTATGGCTGATGAAATGGGGCTCGGTAAAACTTTACAGTGTATTGCCCTCATCTGGACTTTACTGCGTCAAGGACCAACAGGTCAACCCATTATAAACAAAGTTGTCATCGTTGCTCCATCAAGTTTAGTTAAAAACTGGTATAATGAACTGAACAAGTGGCTGGGAAGTAGAATCAATGCTGTAGCTATTGACTCAGGCAGCAAAGATGGAATAGACAAACAACTAGTTACTTACATGAGTCAACAAGGCAGTCGTACTCCCACCCCTGTACTGATTATCTCGTACGAGACATTCCGTCTACATGCAGCAGAGCTACACAAGGGCAGTGTTGGGCTGGTCATCTGTGATGAGGGTCACAGGCTGAAGAACCTGGAAAGTCAGACTTACCAAGCATTGAACAAACTGAATACCACTAAGCGTGTTCTTCTTTCAGGTACTCCAATCCAAAACGACTTGCTGGAATATTTTAGCTTGGTACACTTTGTTAATGAAGGAATTTTAGGTTCAGTATcagaattcaaaagaaaatttgagaTTCCAATCTTGAGAGGCAGAGATGCCGATGCGTCAGATAAGGACCATAAAACAGGAACTGAAAAACTGAATGAGCTTATTCTGCTagtaaataaatgtattataaGAAGAACAGCATCAATTCTGTCAAAATATCTACCAATCAAGGTGGAACAAGTGGTATGTTGTCACCTCACTCACCTTCAAACCCAGCTTTACAAACATTTAGTCCAGTCAAACGTGGCGCAACGGCTACAGAAAGTAGAATCAAAGAGTGGCGGTGTGTCTGCTTCTTCACTGGGTTTTATCACTAATCTCAAGAAACTGTGCAATCATCCAGAACTTATCTTTGAGAAGGCAAAGTTGCAGGAAGAGGGCTTTAGAGGTGCTTTACAGATCTTTCCCAATGGATTTTCTGACAAGCAAAATTTACTTCCTGATTTATCAgGTAAAATGCAAGTACTTGACTACATTCTGGCCATGACTAAATCAACTACAGATGACAAAGTTGTGTTGGTATCAAACTACACTCAAACACTGGACATCTTTGAAAAGCTCTGCAGACAAAGAAActATCAGTACGTTCGTCTTGATGGTAGTATGTCAATCAAGAAAAGACAGAAGATAGTAGACAAGTTCAATGATCCTAAGGGTGgtgatttcattttcatgcTCAGTAGTAAAGCAGGAGGCTGCGGCCTGAACCTGATTGGTGCAAACAGACTAGTGATGTTTGATCCTGACTGGAATCCTGCCAATGATGACCAGGCCATGGCTAGAGTATGGAGAGATGGTCAGAAGAAAAAGgtATTCATATACAGGCTTCTATCAACTGGAACCATAGAAGAAAAGATCTTCCAACGTCAAGCCCACAAGAAGGCTCTTAGCAGCTGTGTAGTAGATGAAGAGGAAGATGTTGAGAAACACTTCTCACTTGAACAGCTGAGAGATTTATTTCGCTTGAATGAAGATACCCTGAGTGATACTCATGACAAGTTCAAGTGTCGTCGATGTGTGAACAACATTCAGGTACAACCCCCCTCCGAGGACAAGAACTGCAGTGCAAGTCTCGCCCAATGGAACCATTCTGCAAGTAGTAAAAACCTAGAAGatattatattaaaacaaGCCTGGAAGTGTGGAGTCAGTTTTGTATTCCATCAAAAATCCCATGACAAACAACTTGGAGTATCTATTAGATAGCAGCATTCTTCTATAGTCAGGTATCTTAAATGCTCAACTTTTGAAGGAAATTTTAATTACACCTTGTTAGAGTTCAATAATGCAAAGTACATGACTCTTCAATATCAACTAACAGGTTCTGCTTTCATCATGATATTTTGTCAAAAGCCACGAATTCTGATTGGATCGATTCGGGAACAACCTCTCCTATTTCAACTTCTATTCTTTGactagaccttttcagcttgggtATTTTCCAATAACTGTTTTAGTTAAAACTCATGACAAAGGCCAATAtggatatattttattcttccaATGCCGTCAATGTAAACCGATAACTGGCGACTCAAAAtcacaataagttttgtattgcAATTCTCCTATCACCAGATAATTCTGACCCGAAGGAGAATTGCAtactatttaatatttatttttgttcagcaaaaaaaattattcaatgacAACTAGATAATTTGATAAACCTCCAAGATTTTaaccataaatataataatca

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
F1Q8K0	DNA repair and recombination protein RAD54-like OS=Danio rerio OX=7955 GN=rad54l PE=1 SV=1
O12944	DNA repair and recombination protein RAD54-like (Fragment) OS=Gallus gallus OX=9031 GN=RAD54L PE=2 SV=1
P70270	DNA repair and recombination protein RAD54-like OS=Mus musculus OX=10090 GN=Rad54l PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001215 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF00176 all species →	SNF2-rel_dom	SNF2-related domain	Domain	Interproscan
PF08658 all species →	Rad54_N	Rad54 N terminal	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR038718 all species →	Homologous_superfamily	SNF2-like, N-terminal domain superfamily	Interproscan
IPR049730 all species →	Domain	SNF2/RAD5-like, C-terminal helicase domain	Interproscan
IPR050496 all species →	Family	SNF2/RAD54 Helicase and DNA Repair	Interproscan
IPR000330 all species →	Domain	SNF2, N-terminal	Interproscan
IPR013967 all species →	Domain	Rad54, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45629 all species →	SNF2/RAD54 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0015616 all species →	Molecular Function	DNA translocase activity	Interproscan
GO:0045003 all species →	Biological Process	double-strand break repair via synthesis-dependent strand annealing	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0140658 all species →	Molecular Function	ATP-dependent chromatin remodeler activity	Interproscan
GO:0016817 all species →	Molecular Function	hydrolase activity, acting on acid anhydrides	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
K10875	RAD54L, RAD54; DNA repair and recombination protein RAD54 and RAD54-like protein	EC:5.6.2.-	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 Anthopleura xanthogrammica 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 Anthopleura xanthogrammica, 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 →