Gene detail

Detailed information of CAB3987149.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3987149.1, DNA ligase 4 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3987149.1 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
Q90YB1	DNA ligase 4 OS=Gallus gallus OX=9031 GN=LIG4 PE=2 SV=2
Q8BTF7	DNA ligase 4 OS=Mus musculus OX=10090 GN=Lig4 PE=2 SV=2
Q5R6L3	DNA ligase 4 OS=Pongo abelii OX=9601 GN=LIG4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002879 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01068 all species →	DNA_ligase_A_M	ATP dependent DNA ligase domain	Domain	Interproscan
PF11411 all species →	DNA_ligase_IV	DNA ligase IV	Family	Interproscan
PF16589 all species →	BRCT_2	BRCT domain, a BRCA1 C-terminus domain	Family	Interproscan
PF04679 all species →	DNA_ligase_A_C	ATP dependent DNA ligase C terminal region	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR021536 all species →	Domain	DNA ligase IV domain	Interproscan
IPR029710 all species →	Family	DNA ligase 4	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45997 all species →	DNA LIGASE 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005958 all species →	Cellular Component	DNA-dependent protein kinase-DNA ligase 4 complex	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0032807 all species →	Cellular Component	DNA ligase IV complex	Interproscan
GO:0051103 all species →	Biological Process	DNA ligation involved in DNA repair	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 CAB3987149.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3987149.1 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

8TPM > 0

4Conditions

8.6Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	3.25	8.58
apical branchlet · Temperature treatment at T0	6	2	1.53	5.33
apical branchlet · Temperature treatment at T25	5	1	0.32	1.60
apical branchlet · Control at T0	4	1	1.05	4.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.58
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.37
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.53
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.00
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
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.33
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.87
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	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	1.60
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	4.18
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.