Gene detail

Detailed information of CAB4013789.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4013789.1, lysine-specific demethylase 4B-like, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4013789.1 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
Q8VCD7	Lysine-specific demethylase 4C OS=Mus musculus OX=10090 GN=Kdm4c PE=1 SV=1
Q9H3R0	Lysine-specific demethylase 4C OS=Homo sapiens OX=9606 GN=KDM4C PE=1 SV=2
Q91VY5	Lysine-specific demethylase 4B OS=Mus musculus OX=10090 GN=Kdm4b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006820 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02373 all species →	JmjC	JmjC domain, hydroxylase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003347 all species →	Domain	JmjC domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10694 all species →	LYSINE-SPECIFIC DEMETHYLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0032452 all species →	Molecular Function	histone demethylase activity	Interproscan
GO:0032454 all species →	Molecular Function	histone H3K9 demethylase activity	Interproscan
GO:0051864 all species →	Molecular Function	histone H3K36 demethylase 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
K06709	KDM4, JMJD2, JHDM3; [histone H3]-trimethyl-L-lysine9/36 demethylase	EC:1.14.11.66 EC:1.14.11.69	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4013789.1 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

213.3Max TPM

31.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	65.50	213.30
apical branchlet · Temperature treatment at T0	6	4	29.86	101.26
apical branchlet · Temperature treatment at T25	5	2	13.57	53.15
apical branchlet · Control at T0	4	1	6.30	25.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	213.30
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	103.82
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	49.39
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	26.48
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	101.26
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	53.29
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	16.19
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	8.44
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
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	53.15
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	14.71
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
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	25.18
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.