Gene detail

Detailed information of CAB4029841.1 in Paramuricea clavata

Genomic Location: pcla8_s017627:121...2246
NR annotation: CAB4029841.1, E3 ubiquitin- ligase NRDP1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A032879

TTCAGGCGAACAGAGAATAAATATGGCATCAAATTATTCACTTGGATATGATGACGAGAGATTCGAGTCGATAGTAGACCAAAATTTCCACTGTTTGATTTGCTATAACGTATTGAAAGACCCGGTAATGTGTCGGAGAAACCAGCACTATTTCTGCCACGGCTGTATCACGGAACATCTTCGTACGAATTCCCATACATGCCCAACATGCGCTGACGAGCTGAGTGTCGAAACATTGGCGGAAGTCCCAAGAATTGTGAAGAATTACTTGGAtgaacgaaaaattcgttgcgATCATTACGACAGAGGATGTCGAGAACTCGTACAGCTGCAGAATTTAAAGCGACATGTCGCCGAATGCGGGTTTACTCCAGTCGTTTGTGGAAATCAAGGTTGTGGTGAGACAATCAGTAAAAGAGATCGTACATATCACGAGAGTGAACTGTGTCAATTTAGAAAGTTGAAGTGTCACAACTGTGGAGAAATCAGCACGATGATAGCGGGCATGCAAACGGAAATCGCAAATCAGAACACGAAAATCAACGCAGAAATGGCACACACGAACACGAAATTGAAAAACGTGGACACGAAAATAGTACACATCGACACGAAACTGGAAAACATGGACACAAAAATGGCAAATTGGCAAGCCAACGTGGAAGCGAGGTTCGAAGCGAGGTTCGAAGCGATGAATAATGAAGTGAGAGGAATGAAAATGAGTTTAAATGAAGTAAAAGATGGTTTTGATCACTTGAAAGAAGCAGTACTTGAGAAGATAGAGAGCAAAGAAAGAAAGCAGGAGGAAATCACAAGAGATGTAAGTGGCACAGCGAGTGGCGGGAGGGAAAATCAACATATATTTGTTGCTGGTGGTCGGGGGAGAAACTCGCTAGAAATATTTAACTACCGTCAGAGATTGTGGTCTTTATTAAAGCCGATGCTAGTGAGTCGTTGCAGCGCATCTTCATTTTTTCACAATAATCATGTGACTGTAGCGGGAGGTTATTGTCGTGGTTTTGTAGATAACATGATCCGAATGAACATTCACCCAGTCCCTGATCTCTCAATTAACTGGAGTGATTTTGCTGCCAAACTTCCTGCCAAGATGTGTGGACACAGCAGTGTGGTGTACAAGGATAGCTTGTTGGTTACTGGAGGTTATGATGCAGATCAATGTGTCTACTCTGACTGTATTCATGAAGTCCAACTTAAACCACCCCACAATGTTCAACTGGTATGCAAGATGCCTGAACCAAGAGCTCGTCACAGCACAGTACTGTGTGATGATAGTATTTTGATCGTTGGGGGAAAGAAATCATTGGACTGCGAAGACAACCTCAGCAGTGTGTTAAGCTATGACATCAAGAAGAATGAATGTCAACAGTTACCTGCGCTTCCCTATCCAGTGAGTGAAATGGCGACAGTCAAGTGGGCTGAGAATGTCGTGATCATTGGTGGGATTGACAAGGATGGTAATGTATTAAACAATGTTATAATTTATAACACGAAGACTGGAAACAGTCATATGTTGCCTCCCATGTTACACAAGAGGAAAGGATGTATGGCAGTTGTTATTGAGAATACAATTGTAGTACTAGGAGGCGCGGATGAAAAAAGGAATGATTTGAAATCAGTTGAAGGTTTCAATTTTGAACGATTTTCATGGCAGGAACTTCCTGACATGAAGGAAAAAAGATGCTTCGCTACAGCTGTTGTGATCTAGACATGCTTGTATATATTATGTACAATATTTGACATATACGTCAAAACTTTATCCAGATTTTATAGCATATGGATTAAAGAACTGCCTTACTCTAAGCGCTACAATGTTGTAATATAGATATCATTGAGTAAAAATTCATGCCTACAGTATATACTGTTTAAAGATTGTGTTTATCTGAGTAAGCAATCTCTGATGATTTCAGTAAAGAAACTTCATCTCGTTATACTAGAGACCTTTCTCTAACTTTCTAACTTATAGATTTATTCAATTGATTGCCTCACAtgaacttaaaatttatatcaaaatatgacCTCCACAAGAGGGGAAAGTCTGGGAATGAGGTCGACATCAAGCTGTTGAGCATACGCGCTATTTtagtttaaaattaataaaacagccCAGT

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000354 (this species only)
Ubiquitin family	E3\|E3 activity RING\|U-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13418 all species →	Kelch_4	Galactose oxidase, central domain	Repeat	Interproscan
PF01344 all species →	Kelch_1	Kelch motif	Repeat	Interproscan
PF13923 all species →	zf-C3HC4_2	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF02176 all species →	zf-TRAF	TRAF-type zinc finger	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051746 all species →	Family	Kelch domain-containing protein 8	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR006652 all species →	Repeat	Kelch repeat type 1	Interproscan
IPR001293 all species →	Domain	Zinc finger, TRAF-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46260 all species →	RING-TYPE DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion 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
K15682	PDZRN3_4, LNX3_4; ligand of Numb protein X 3/4	EC:2.3.2.27	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4029841.1 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

10TPM > 0

4Conditions

5.8Max TPM

1.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	1.59	3.86
apical branchlet · Temperature treatment at T0	6	4	1.82	5.77
apical branchlet · Temperature treatment at T25	5	1	0.00	0.00
apical branchlet · Control at T0	4	1	0.37	1.48

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	3.86
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.56
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.03
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.09
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
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.77
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.56
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.70
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.89
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	0.00
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	1.48
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.