Gene detail

Detailed information of CAB4025060.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4025060.1, LIM domain-binding 2-like isoform X4 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4025060.1 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
Q9W676	LIM domain-binding protein 2 OS=Gallus gallus OX=9031 GN=LDB2 PE=2 SV=1
Q6NVL6	LIM domain-binding protein 1 OS=Xenopus tropicalis OX=8364 GN=ldb1 PE=2 SV=1
O43679	LIM domain-binding protein 2 OS=Homo sapiens OX=9606 GN=LDB2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001819 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17916 all species →	LID	LIM interaction domain (LID)	Domain	Interproscan
PF01803 all species →	LIM_bind	LIM-domain binding protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029005 all species →	Family	LIM-domain binding protein/SEUSS	Interproscan
IPR041363 all species →	Domain	LIM interaction domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10378 all species →	LIM DOMAIN-BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000122 all species →	Biological Process	negative regulation of transcription by RNA polymerase II	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0007399 all species →	Biological Process	nervous system development	Interproscan
GO:0030274 all species →	Molecular Function	LIM domain binding	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	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
K24143	LDB2; LIM domain-binding protein 2	-	Domain-containing proteins not elsewhere classified	ko04990	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4025060.1 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

13TPM > 0

4Conditions

71.0Max TPM

18.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	28.01	67.49
apical branchlet · Temperature treatment at T0	6	4	23.05	70.95
apical branchlet · Temperature treatment at T25	5	2	15.47	60.72
apical branchlet · Control at T0	4	1	3.03	12.11

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	67.49
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	43.42
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	28.18
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	14.81
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.58
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	6.60
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	70.95
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	43.78
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	16.76
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.82
SRR19977426	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
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	60.72
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	16.64
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
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	12.11
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.