Gene detail

Detailed information of CAB4007236.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4007236.1, sorting nexin-6, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4007236.1 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
A0A8J1LLF7	Endoribonuclease Dicer-S OS=Xenopus laevis OX=8355 GN=dicer1.S PE=3 SV=1
A0A974H8H3	Endoribonuclease Dicer-L OS=Xenopus laevis OX=8355 GN=dicer1.L PE=2 SV=1
B3DLA6	Endoribonuclease Dicer OS=Xenopus tropicalis OX=8364 GN=dicer1 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006318 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF20930 all species →	Dicer_PBD	Dicer, partner-binding domain	Domain	Interproscan
PF20932 all species →	Dicer_dsRBD	Dicer, dsRNA-binding domain	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF20931 all species →	Dicer_platform	Dicer, platform domain	Domain	Interproscan
PF00636 all species →	Ribonuclease_3	Ribonuclease III domain	Family	Interproscan
PF03368 all species →	Dicer_dimer	Dicer dimerisation domain	Domain	Interproscan
PF00787 all species →	PX	PX domain	Domain	Interproscan
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan
PF09325 all species →	Vps5	Vps5 C terminal like	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048513 all species →	Domain	Dicer, partner-binding domain	Interproscan
IPR027267 all species →	Homologous_superfamily	AH/BAR domain superfamily	Interproscan
IPR044441 all species →	Domain	Dicer, double-stranded RNA-binding domain	Interproscan
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR000999 all species →	Domain	Ribonuclease III domain	Interproscan
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR036389 all species →	Homologous_superfamily	Ribonuclease III, endonuclease domain superfamily	Interproscan
IPR003100 all species →	Domain	PAZ domain	Interproscan
IPR048512 all species →	Domain	Dicer, platform domain	Interproscan
IPR038248 all species →	Homologous_superfamily	Dicer dimerisation domain superfamily	Interproscan
IPR005034 all species →	Domain	Dicer dimerisation domain	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan
IPR015404 all species →	Domain	Sorting nexin/Vps5-like, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14950 all species →	DICER-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0030422 all species →	Biological Process	siRNA processing	Interproscan
GO:0031054 all species →	Biological Process	pre-miRNA processing	Interproscan
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0004525 all species →	Molecular Function	ribonuclease III activity	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016442 all species →	Cellular Component	RISC complex	Interproscan
GO:0090501 all species →	Biological Process	obsolete RNA phosphodiester bond hydrolysis	Interproscan
GO:0016891 all species →	Molecular Function	RNA endonuclease activity, producing 5'-phosphomonoesters	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase 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

No KEGG orthology assignment for CAB4007236.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4007236.1 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

25.0Max TPM

7.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	14.28	25.00
apical branchlet · Temperature treatment at T0	6	5	5.37	12.41
apical branchlet · Temperature treatment at T25	5	5	4.75	12.73
apical branchlet · Control at T0	4	2	3.61	13.07

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	25.00
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	14.57
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.14
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	12.00
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.86
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	9.11
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.41
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.73
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.92
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.79
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.37
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	12.73
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	5.61
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.45
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.44
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.52
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	13.07
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	1.35
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.