Gene detail

Detailed information of CAB3977345.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3977345.1, helicase SKI2W-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3977345.1 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
Q15477	Superkiller complex protein 2 OS=Homo sapiens OX=9606 GN=SKIC2 PE=1 SV=3
Q6NZR5	Superkiller complex protein 2 OS=Mus musculus OX=10090 GN=Skic2 PE=2 SV=1
O59801	Putative ATP-dependent RNA helicase C550.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPCC550.03c PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001225 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21408 all species →	MTR4-like_stalk	Exosome RNA helicase MTR4-like, stalk	Domain	Interproscan
PF08148 all species →	DSHCT	DSHCT (NUC185) domain	Domain	Interproscan
PF17911 all species →	Ski2_N	Ski2 N-terminal region	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF13234 all species →	MTR4_beta-barrel	Mtr4-like, beta-barrel domain	Domain	Interproscan
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR050699 all species →	Family	RNA/DNA Helicase	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR048392 all species →	Domain	Exosome RNA helicase MTR4-like, stalk	Interproscan
IPR012961 all species →	Domain	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Interproscan
IPR040801 all species →	Domain	Ski2, N-terminal domain	Interproscan
IPR025696 all species →	Domain	Exosome RNA helicase MTR4-like, beta-barrel domain	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR016438 all species →	Family	ATP-dependent RNA helicase SKI2-like	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12131 all species →	ATP-DEPENDENT RNA AND DNA HELICASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0006401 all species →	Biological Process	RNA catabolic process	Interproscan
GO:0055087 all species →	Cellular Component	Ski complex	Interproscan
GO:0070478 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	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
K12599	SKI2, SKIV2L; antiviral helicase SKI2	EC:5.6.2.6	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 CAB3977345.1 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

22.1Max TPM

3.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	7.32	22.09
apical branchlet · Temperature treatment at T0	6	4	2.84	8.05
apical branchlet · Temperature treatment at T25	5	1	0.43	2.13
apical branchlet · Control at T0	4	2	1.98	6.05

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	22.09
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	12.87
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.28
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.67
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	8.05
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.85
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.03
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.11
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
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.13
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	6.05
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	1.86
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.