Gene detail

Detailed information of CAB4002248.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4002248.1, Hypothetical predicted protein [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4002248.1 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
Q498K9	Protein LSM14 homolog B-B OS=Xenopus laevis OX=8355 GN=lsm14b-b PE=1 SV=1
Q566L7	Protein LSM14 homolog B OS=Xenopus tropicalis OX=8364 GN=lsm14b PE=2 SV=1
Q8CGC4	Protein LSM14 homolog B OS=Mus musculus OX=10090 GN=Lsm14b PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007671 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12701 all species →	LSM14	Scd6-like Sm domain	Domain	Interproscan
PF09532 all species →	FDF	FDF domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR025762 all species →	Domain	DFDF domain	Interproscan
IPR025768 all species →	Domain	TFG box	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR025609 all species →	Domain	Lsm14-like, N-terminal	Interproscan
IPR025761 all species →	Domain	FFD box	Interproscan
IPR019050 all species →	Domain	FDF domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13586 all species →	SCD6 PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0033962 all species →	Biological Process	P-body assembly	Interproscan
GO:0034063 all species →	Biological Process	stress granule assembly	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
K18749	LSM14, RAP55, SCD6; protein LSM14	-	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4002248.1 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

18TPM > 0

4Conditions

31.7Max TPM

3.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	0.71	1.26
apical branchlet · Temperature treatment at T0	6	6	8.17	31.69
apical branchlet · Temperature treatment at T25	5	4	3.67	10.21
apical branchlet · Control at T0	4	3	0.80	2.38

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.26
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.99
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.89
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.71
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.43
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	31.69
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.84
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.15
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.62
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.61
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.14
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	10.21
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	5.31
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.69
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.16
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	2.38
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.72
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.10
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.