Gene detail

Detailed information of XP_068677791.1 in Montipora foliosa

Genomic Location: chr11:5026923...5048568
NR annotation: XP_029184621.2, DNA repair protein RAD51 homolog 3-like isoform X1 [Acropora millepora]
Species Montipora foliosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068821690.1

TCGGTCAAACTATCGCGCCAATCCTAAAATATTTGACAAGGTGTCTCCCTTTCTCGTAGAGAATCGATTACATGAGGAGAGGAGTTAGGTAGCATCTTTTAAATGCAACGAGAATTATCCACATTCCCTTTGTCTCCAAGTTACGTGCAGAAGTTGTCGAATGCAGGTTATTTTACAGCAGATGACCTGAAAGATGTCAGCCCAACTGAACTAAGTGAAGACCTAGGTGTGGAAagagaagaagctcttaggatTATTCAAACAGTCCGGAGCTCTACCAACCCAGAGAACAAGTCACCAGTTACCATATCAAAGACAAACAATGAAATTAGATCAAATGCCATCCCAGGAAGCAAGAATGCTTATGACCTCTTGCTACAGGAGCAATCATGTGGAAGCATTGTCACATTCTGTGAGCAACTTGACGACATGTTAGGTGGTGGTGTACCTGTGGGAAAGATCACCGAGTTTTGTGGTGCACCAGGAATTGGCAAGACACAGATAGGTATGCAGCTTGCAGTTGATGTACAAATTCCTGATGAGTTTGGTGGCCTTAATGGAGAAGCAATCTATATTGAAAAATCTCTTCAAATGGAAGCTATGAAAAAGTTTCAAGTGGAAAACATCCTATCCAAAATCTATGTGTTTAGATGCCATGACTATATGCAGCTTATTGCATTGTCACATGTGTTATCAGACTTCTTGACAGAACACCCTAAGGTTAAACTCATCGTTGTGGATAGTATTGCTTTTCAGTTCCGACATGACTTTGATGACCTCGCTTTGAGGACGAGGCTTTTAAATGGTTTGGCACAGAGTTTCATCAAGATGGCTTGTGAAAATCAGTTAGCTGTCGTTTTCATGAACCAGATGACCACTCGAATCAAAACCTCGCAGTTTGAACAGTCTCACCTGATACCTGCGCTAGGTGAAAGCTGGGGTCACGCTAGCACAATTCGAATTGTTTTGTActgggaggaaaaccagagGTTTGCAAACTTGTACAAGTCGCCTTCACGTCAAGAAATGACCGTTCCCTTCCAAATCACGGGAGACGGCGTTCGAGACTGTTTTTCAAACATCGCAGAACACAACCACTTGGAAAATGAAAACGTCGGGCATGCTCAAGAAAACTATCAAGGTGACACACGGGATACCCACGTGAAAGCAGAGGCGACCAGTACCTCAATGACTCGGAAAAGAAGATTTGAAGAACTCTCGTAGGTCCGCATTAAGTGGAAATAGTGAGACAAGGCAGTGCTATCGGTCTCAAAACATTGCCTTCATGTTTTCTGTTGCCACGATCAATTCAGGCCCTTAGGCGCTGAGATATTTTTTTCAGGGTTCGTGCAGTTGACAGCAATTCCATAACAGCTGGataaattcttctttttctttggatttcaaaactatgttaacttaacactaagTGAACCAAGTTTCAAGTTCTAATTTTGAAAAGACAGGTGTctattttaactgaaattttcatatttattggtccgctattactaactttaacatcttgagagagctgggtggaggagaaaatgacgtcaaagactcgatagtttaagaatgcaatgcgtaaGTAATGGCCGACCGtggaatccaaaacttacactcaaagtaagcaACCttcggataaaaatcaaagctcaaaattttgccagtcatgtGTTAAGCAAACCCGCTTTCAAAACTTGAAGAAATAAAGTAGCACTTTCAAGGGCGGATTTAGGGGTGAGCCCAGCGGGCCCCGGCCTTCCCCCACCCCTTTTGtccaggattttttttcttttgtcaacGTGTGTCGGATGGTACTTCGAGCTTTGGtacttaaatatattttgtttaataaaCATTGTTGATAAGAAAAGTTATCGTAGGCTGTTCAAATCAACGGcccttattactgggttgccataggcaacctAGTCATAAATTAGCTAAATTTTTCCGTTTtcgtttttttccgtgtcgggaaaagtctttcctgtccgCCGTctcaaatcgacacggtttcggcaacagtctcgatcggtgtcgtgtaaacagaagctGTAACCGCATCGATAACGATgaggttacaaatgaaaccgcgttcgtgtaaacgctgccacAGACGCAAGGCCACAGCCCACAATGACAAACCAAACAAACCGGACAATCACGAACACATTGCCAACTACTGGTTTGCATCAGTTAGGTCCTTCCGCTTTCC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q924H5	DNA repair protein RAD51 homolog 3 OS=Mus musculus OX=10090 GN=Rad51c PE=1 SV=1
Q8R2J9	DNA repair protein RAD51 homolog 3 OS=Cricetulus griseus OX=10029 GN=RAD51C PE=2 SV=1
O43502	DNA repair protein RAD51 homolog 3 OS=Homo sapiens OX=9606 GN=RAD51C PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005842 (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
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
IPR052093 all species →	Family	Homologous Recombination Repair Mediator	Interproscan
IPR010995 all species →	Homologous_superfamily	DNA repair Rad51/transcription factor NusA, alpha-helical	Interproscan
IPR016467 all species →	Family	DNA recombination and repair protein, RecA-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46239 all species →	DNA REPAIR PROTEIN RAD51 HOMOLOG 3 RAD51C	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:0000707 all species →	Biological Process	meiotic DNA recombinase assembly	Interproscan
GO:0005657 all species →	Cellular Component	replication fork	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0008821 all species →	Molecular Function	crossover junction DNA endonuclease activity	Interproscan
GO:0033063 all species →	Cellular Component	Rad51B-Rad51C-Rad51D-XRCC2 complex	Interproscan
GO:0033065 all species →	Cellular Component	Rad51C-XRCC3 complex	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	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
K10870	RAD51L2, RAD51C; RAD51-like protein 2	-	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068677791.1 across 36 RNA-seq samples of Montipora foliosa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

36Samples

28TPM > 0

1Conditions

13.3Max TPM

5.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	28	5.67	13.33

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12710845	Polyps	Polyps	OA4 day3	not recorded	SRP199550	13.33
SRR12959238	Polyps	Polyps	E4 day0	not recorded	SRP199550	10.50
SRR27940180	Polyps	Polyps	not recorded	not recorded	SRP199550	9.99
SRR12904780	Polyps	Polyps	not recorded	not recorded	SRP199550	9.90
SRR12786895	Polyps	Polyps	OA4 day0	not recorded	SRP199550	9.64
SRR12904791	Polyps	Polyps	not recorded	not recorded	SRP199550	9.39
SRR12959211	Polyps	Polyps	E4 day9	not recorded	SRP199550	9.30
SRR12959226	Polyps	Polyps	E4 day3	not recorded	SRP199550	9.24
SRR27940177	Polyps	Polyps	not recorded	not recorded	SRP199550	9.16
SRR27940179	Polyps	Polyps	not recorded	not recorded	SRP199550	8.88
SRR12959224	Polyps	Polyps	E4 day3	not recorded	SRP199550	8.84
SRR12904792	Polyps	Polyps	not recorded	not recorded	SRP199550	8.76
SRR12959237	Polyps	Polyps	E4 day0	not recorded	SRP199550	8.13
SRR12959225	Polyps	Polyps	E4 day3	not recorded	SRP199550	7.36
SRR12786904	Polyps	Polyps	OA4 day0	not recorded	SRP199550	7.36
SRR12959212	Polyps	Polyps	E4 day9	not recorded	SRP199550	7.13
SRR12959181	Polyps	Polyps	E4 day0	not recorded	SRP199550	6.90
SRR12959198	Polyps	Polyps	E4 day15	not recorded	SRP199550	6.09
SRR12959199	Polyps	Polyps	E4 day15	not recorded	SRP199550	5.99
SRR12959200	Polyps	Polyps	E4 day15	not recorded	SRP199550	5.95
SRR12710865	Polyps	Polyps	OA4 day3	not recorded	SRP199550	5.48
SRR12959213	Polyps	Polyps	E4 day9	not recorded	SRP199550	5.44
SRR12710866	Polyps	Polyps	OA4 day3	not recorded	SRP199550	5.10
SRR12959185	Polyps	Polyps	E4 day21	not recorded	SRP199550	4.23
SRR12959186	Polyps	Polyps	E4 day21	not recorded	SRP199550	3.70
SRR12710853	Polyps	Polyps	OA4 day9	not recorded	SRP199550	3.30
SRR12710852	Polyps	Polyps	OA4 day9	not recorded	SRP199550	3.24
SRR12959187	Polyps	Polyps	E4 day21	not recorded	SRP199550	1.69
SRR12710854	Polyps	Polyps	OA4 day9	not recorded	SRP199550	0.00
SRR12786903	Polyps	Polyps	OA4 day0	not recorded	SRP199550	0.00
SRR12807380	Polyps	Polyps	OA4 day0	not recorded	SRP199550	0.00
SRR12849112	Polyps	Polyps	OA4 day0	not recorded	SRP199550	0.00
SRR12927879	Polyps	Polyps	E4 day0	not recorded	SRP199550	0.00
SRR12963483	Polyps	Polyps	E4 day0	not recorded	SRP199550	0.00
SRR9129315	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613518	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MFOLI_TPM, StringTie quantification over 36 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora foliosa 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	32	XP_068678157.1	0.947235244104995
Negatively correlated	5	XP_068681185.1	-0.415211553796183

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora foliosa, 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.	ready	open →
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 →