Gene detail

Detailed information of CAB3998693.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3998693.1, DNA repair complementing XP-C cells [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3998693.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P51612	DNA repair protein complementing XP-C cells homolog OS=Mus musculus OX=10090 GN=Xpc PE=1 SV=2
Q01831	DNA repair protein complementing XP-C cells OS=Homo sapiens OX=9606 GN=XPC PE=1 SV=4
Q24595	DNA repair protein complementing XP-C cells homolog OS=Drosophila melanogaster OX=7227 GN=Xpc PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004584 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03835 all species →	Rad4	Rad4 transglutaminase-like domain	Domain	Interproscan
PF10405 all species →	BHD_3	Rad4 beta-hairpin domain 3	Domain	Interproscan
PF10404 all species →	BHD_2	Rad4 beta-hairpin domain 2	Domain	Interproscan
PF10403 all species →	BHD_1	Rad4 beta-hairpin domain 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004583 all species →	Family	DNA repair protein Rad4	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR018326 all species →	Domain	Rad4 beta-hairpin domain 1	Interproscan
IPR018026 all species →	Family	DNA repair protein Rad4-like	Interproscan
IPR018328 all species →	Domain	Rad4 beta-hairpin domain 3	Interproscan
IPR036985 all species →	Homologous_superfamily	Transglutaminase-like superfamily	Interproscan
IPR018325 all species →	Domain	Rad4/PNGase transglutaminase-like fold	Interproscan
IPR018327 all species →	Domain	Rad4 beta-hairpin domain 2	Interproscan
IPR042488 all species →	Homologous_superfamily	Rad4, beta-hairpin domain 3 superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12135 all species →	DNA REPAIR PROTEIN XP-C / RAD4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000111 all species →	Cellular Component	nucleotide-excision repair factor 2 complex	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0071942 all species →	Cellular Component	XPC complex	Interproscan
GO:0003677 all species →	Molecular Function	DNA 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
K10838	XPC; xeroderma pigmentosum group C-complementing protein	-	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 CAB3998693.1 across 21 RNA-seq samples of Paramuricea clavata. 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

11TPM > 0

4Conditions

33.0Max TPM

6.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	9.80	28.50
apical branchlet · Temperature treatment at T0	6	5	10.45	33.01
apical branchlet · Temperature treatment at T25	5	1	0.27	1.36
apical branchlet · Control at T0	4	1	1.34	5.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	28.50
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.47
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	12.48
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	4.33
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	33.01
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	17.38
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	8.51
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.31
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.46
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.36
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	5.34
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

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.