Gene detail

Detailed information of CAB4018660.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4018660.1, DNA polymerase beta [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4018660.1 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
Q27958	DNA polymerase beta OS=Bos taurus OX=9913 GN=POLB PE=2 SV=3
P06746	DNA polymerase beta OS=Homo sapiens OX=9606 GN=POLB PE=1 SV=3
Q8K409	DNA polymerase beta OS=Mus musculus OX=10090 GN=Polb PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001983 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14791 all species →	DNA_pol_B_thumb	DNA polymerase beta thumb	Family	Interproscan
PF10391 all species →	DNA_pol_lambd_f	Fingers domain of DNA polymerase lambda	Domain	Interproscan
PF14792 all species →	DNA_pol_B_palm	DNA polymerase beta palm	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002054 all species →	Domain	DNA-directed DNA polymerase X	Interproscan
IPR029398 all species →	Domain	DNA polymerase beta, thumb domain	Interproscan
IPR027421 all species →	Homologous_superfamily	DNA polymerase lambda lyase domain superfamily	Interproscan
IPR018944 all species →	Domain	DNA polymerase lambda, fingers domain	Interproscan
IPR043519 all species →	Homologous_superfamily	Nucleotidyltransferase superfamily	Interproscan
IPR022312 all species →	Family	DNA polymerase family X	Interproscan
IPR002008 all species →	Family	DNA polymerase family X, beta-like	Interproscan
IPR028207 all species →	Domain	DNA polymerase beta, palm domain	Interproscan
IPR019843 all species →	Binding_site	DNA polymerase family X, binding site	Interproscan
IPR037160 all species →	Homologous_superfamily	DNA polymerase, thumb domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11276 all species →	DNA POLYMERASE TYPE-X FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0034061 all species →	Molecular Function	DNA polymerase activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0016779 all species →	Molecular Function	nucleotidyltransferase 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
K02330	POLB; DNA polymerase beta	EC:2.7.7.7 EC:4.2.99.-	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 CAB4018660.1 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

10TPM > 0

4Conditions

16.2Max TPM

3.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	7.38	16.18
apical branchlet · Temperature treatment at T0	6	3	4.07	11.12
apical branchlet · Temperature treatment at T25	5	1	0.31	1.53
apical branchlet · Control at T0	4	1	2.73	10.93

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	16.18
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.20
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.11
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.57
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.22
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	11.12
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.93
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.35
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977437	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	1.53
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	10.93
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.