Gene detail

Detailed information of CAB3979606.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: XP_046856392.1, U6 snRNA-associated Sm-like protein LSm6 [Xenia sp. Carnegie-2017]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3979606.1 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
P62312	U6 snRNA-associated Sm-like protein LSm6 OS=Homo sapiens OX=9606 GN=LSM6 PE=1 SV=1
P62313	U6 snRNA-associated Sm-like protein LSm6 OS=Mus musculus OX=10090 GN=Lsm6 PE=1 SV=1
Q9M1Z3	Sm-like protein LSM6A OS=Arabidopsis thaliana OX=3702 GN=LSM6A PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002962 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01423 all species →	LSM	LSM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR016487 all species →	Family	Sm-like protein Lsm6/SmF	Interproscan
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11021 all species →	SMALL NUCLEAR RIBONUCLEOPROTEIN F SNRNP-F	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0005688 all species →	Cellular Component	U6 snRNP	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0005732 all species →	Cellular Component	sno(s)RNA-containing ribonucleoprotein complex	Interproscan
GO:0030490 all species →	Biological Process	maturation of SSU-rRNA	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	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
K12625	LSM6; U6 snRNA-associated Sm-like protein LSm6	-	Spliceosome	ko03041	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3979606.1 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

12TPM > 0

4Conditions

57.0Max TPM

15.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	29.48	51.59
apical branchlet · Temperature treatment at T0	6	5	22.18	57.03
apical branchlet · Temperature treatment at T25	5	1	2.28	11.40
apical branchlet · Control at T0	4	1	2.09	8.38

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	51.59
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	45.03
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	35.37
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	26.47
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	18.45
SRR19977433	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	57.03
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	38.13
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	19.04
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.82
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.05
SRR19977426	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	11.40
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	8.38
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.