Gene detail

Detailed information of CAB4006937.1 in Paramuricea clavata

Genomic Location: pcla8_s005772:237...2480
NR annotation: CAB4006937.1, DNA repair RAD51 homolog 3 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A041137

GTACTTTTCATCAATATCAGTGTGGATGAACTTCCTTTGAGGTCTGTGACGATAGATTTGTTGTTGGGTGCAGGCTTTCATTCCTGGAGtgattttgacttttcgagCAAGTGACAGCAACAGGCTTGACCGAAGGTATGAAGCGTTAATATAACTGACAGTCGGGTCATATTGAGTGCATTATAATTGGGGCGGGGGGCGGGCAGATAAATTGAGTATAACCCTTTTTACTGAAACCAAAAAAAACTCTTACTTAAAAGGCCCCATCAGCTAGTTTACACTTCCTGACATGCTAGTCTGTATCAATCACTTTGTTCATGAGCTGTATGTCTCACTCCAGCTGCTAGAGTTGTATGCAACATTTGGTCAAGATTTCAGCTCACCCAACatttgggccattccatttattaaGCGCACCCCCATTATTGAGGGTTTTCAAAATATACCCCCTGGATATTGCTTTAGTAATAGGGTATGTGCATAGTATGTGGAtttcgacaactttttaggtaaaaaaattttccagacgagtatgttgcaattgctttccaggtactttatctcaatttttcatacaaaATTTGCTGCAAATTAGCCCCATGGATTTTATTTTTAACTATTACTGTACGTCTGTACTAATAATTGTTTACTGCCATggattttttaacttttttaacatttcatatttttactACCATCAaagatttattttgtttaaattttttccatttggatttttatttggatttttttatatttacccATGgatatatcttgaaaaatttctttctcctaatggattttgttctttGGACCCCCTGGATATTCACAACCCTCAATAGGGGAGGGGGGTGCACATATTAAATGGTATGGCCCTTTGGTAGGAGTGAGATAATAGGTGGTTTACCAACCATCGGACAATCTACAGGGGAGAGTTAAAATTGGACTTTTAAATTAGCCTCTCTTTCATTTATTGCGAGATTGAGTCGACTTGCAAACTCGCTGCAAGTACTTTTACCCAATCCCAAGGCTTGACAGtgtattcaaatagatgcaagcactcgccaGTAAGCACATCAAAGCGCCAGGGACGAGGCTGCTCACAGCAGGCTTGTGTCAGTTGCGTGTGGGTTTTTGAAATGAGTGGAAACAAGGCTTAAATTTAGTCATCGAAAATTCTCCAAAACAAACTGGAAACATGATTGAGTTTGCAAAATGTAAGGTGGCGGATGTTGAGGAGTGCACTTAGTTTATTGGCTTAAGGTTCATTTCCATTGGAGAAATATTCCAGCATCTTGTATATTTTAGAATTAGTGATATTATACCTTTGGACGAAGCAATTGATATTCTTGAAACAGTTGATTATAGTCGAATGATGCTCTGACATTGCATCAAGCCCTAGAAATGGTttcaataaacatgactttgaTGCAGCCATGCAggtttgttttatatttgcttCTGTTGTTGCAGGTCAGTAAAGTATCAAACAAATTAAGGGaccgaataattgttaatataCAAATACCTActcagtggcggacactagaGGGGGcccgagccccccccccccaataattttgaaagactgtaaaaatcttgtaccaaataacataaatcatataacgtaattaatTTTCATATTAAATAGTAAATATTTTATGAAACTTAAGCTATGTGCAATTGCCATTTCCGggatacaaattttaaaaattttccgcatgcccccggacccctgTATAATTCTTGtgtcttccccccccccccaatatttcataaagtgtccacAACTGTACTTTACTGTGTTCAGGTTCTATGAATGGATTTAAAAGCAAAGACCTCATCGATTCTGCTCCGATGAGTGCATTGGAGAACGACATTGACATGACCGACATTCATGCTGCTGGCACAAATGTATCCAGGAATAAAAATGAGAATGTATGTGATACAAGTCAATATGAGAGTGGAAATCACTATGTCTTTCATCCAATCAACGCATGGGAGTTATTTGAACAAGAGAAAAACCGACGTCATATTGTGACGTCTTGTGCCGAGATGGACGACATGTTGGGTGGGGGCGTTGAAACGGGAAAGATCACTGAGTTTTGTGGAGAAAACGAAACTGGAAAATCTCAAATTAGGTAATTAAGGATACTTAGTTAATAACTTCAGAGACGTAGTTTGATGTCCAATGAATTAACTATACCTTtctcaattctatttatttgtCACCAAATACAAGAC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9HJ68	DNA repair and recombination protein RadA OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) OX=273075 GN=radA PE=3 SV=1
Q97BJ9	DNA repair and recombination protein RadA OS=Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) OX=273116 GN=radA PE=3 SV=1
A8AB83	DNA repair and recombination protein RadA OS=Ignicoccus hospitalis (strain KIN4/I / DSM 18386 / JCM 14125) OX=453591 GN=radA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006197 (this species only)

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

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

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

No KEGG orthology assignment for CAB4006937.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4006937.1 across 21 RNA-seq samples of Paramuricea clavata. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

21Samples

0TPM > 0

4Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
apical branchlet · Control at T25	6	0	0.00	0.00
apical branchlet · Temperature treatment at T0	6	0	0.00	0.00
apical branchlet · Temperature treatment at T25	5	0	0.00	0.00
apical branchlet · Control at T0	4	0	0.00	0.00

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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.