Gene detail

Detailed information of CAB4026994.1 in Paramuricea clavata

Genomic Location: pcla8_s015369:155...2199
NR annotation: CAB4026994.1, TNF receptor-associated factor 6-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A042084

GTTGAAGGCGTTGTCGTTCGAAATGGCTTTGAATATGGCTATAAATCCCGACTAATTTCGCTCATACGATGGCTTGTTGCGGTGGCGGTTATCCGGAATATCGTTTTCAAACTTCAGTCGATAAAAATTTCTTCTGTCCAATCTGTACGGATGTATTGAAAGACCCAGTACAATGCCACAACCAACACCTTTTTTGTAGAGCCTGTATAACAGAGCATCTTAAGAATTCCCAGACGTGCCCCGTTTGTATGGAAAAACTCACGGAAGAAGCGTTATCCAAGCCAGCAAGAATTGTGACAGGCTATCTCGATGGTTTGATGGTCAATTGCGAGCACGAGGAACGAGGATGTGTTGAATTGGTCGAGCTTGGCTGTCTTGAAACTCACATTTCCGTGTGCGAGTATAAACCTGTAACGTGTCCTAACGCAAGATGCGAGGCTGTTGTAAACATGGCAGATTTAGACGAACACACGAGCGAGGTTTGTGAATACAGACAAGTATATTGCGAAGAATGTGACGAGAACATGTCTCTCAAGAAATATGGAAAACATGGCTGTTTTATAAGCAAAGATGTTCAGGCAATCAAGGTTGTATTGTTTCAAGTGCAACATCAAGTCAAAGAAATGTCGAACACGCAGAAAGAAATCCTTGAAGCAATCCAAAATCTTACAACTGCTAGTAAAATGAGCACAGTGAAAGGCGAAGCTGCATCCACCAGTGAGACAAAACCGCAAGGGGACATTGTTGTAATTGGTGGACAAAATGGTGTATTGATGAGCAGTAGTTGGCTTGATTCTGTTGAAATGTACTCCCTGGCCAATAGAACATGGACTAAATTGGCACCAATGCAAGAAAAGAGAGCAGCTGCAACTGCACATTTATATAATGGTCGAGTCATGGTTACTGGGGGTCGTTGTGATAGAAGTAATGTAACTAGGAGTATGGAATACGTTCGAGTTCGTGAAGAATCAGAAAAAGATAGTTGGGCCACTGTATTATGTGAAGAATCTGGTTGGGAACCTTTCTTTGCTGAATATGGTCGGTATAAAAGAAGACCAGAGCATCGTAATAGGGGTCACAGAGATGAATTTTCTTCACTTCAATGCAGACTACCATTTCAATGCCTTGGTCACAAAACAGCCATCCTAAATCACCATTTGTGGCTTGTTGGAGGCGTTATTTTTAACGGGCCACAGCGAAGCTTAAATGCCTCCATTCACATGTCACCTATTCATTCACCTCATGCCTATAGCTTTGTGGTCAAGTGTCGAATGCCTAAACCACTTTCATTCCATGGTTTGGAAATAGTTGGCAATGAACTCTTAATCATTGGAGGATCAACGACTGGTAGGATGTGTGATGCTGTTAGCACTGTATTGTCATACAATACAGCAACCAATGCACTCAGAGGATTGCGGCCACTTCCATTTCCAATGCTTGACATGGCAACTGTTAAACATGGTGATGATGTGATCATTATTGGAGGAAGCAACAATGATGATGAGTATTTGAACACAGTTTTCAAGTACAACCATAAGAAGCGTGAATGTGAGCAACTACCAGGAATGAAACACAAGAGGTCTGAATGTGCTGCTGTCATTTCTGGAAACAAAGTGTTTGTGATGGGCGGGTACAACAAAGAGCAAGGATATCTCAGTTCTGTCGAGTGCTTTGATCTTGAGAGTCAGATTTGGCATGAACTTCCATCCATGaatgaagaaaaatataaaatagctGCAGTTTTAGTGCCTTGAGGGATTGCCTTGGTCACCCCCTGGAGGTTTACAGCTAGGGGATGCGATGCTACAACCTGTCTTTTGTCCACCTGCCCTTTGAACAGGTATTTTTGAATGTGGATGGGCAAATAGGTATTCATACCTAAAAACTCCATTTTTTGTCTTAAGGTAATTTTGATATAACATATTGACATTTACCGGGATTAATACAAGCATTTTAATTTGAGTTTTAGTATGAGAGCACTTCCACCAAAACCGCCACCCCCAGAAAACTCTTGATTTTTGGATTGAAGAAATTATTGATTTTGC

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)	OG0000376 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|U-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00097 all species →	zf-C3HC4	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF02176 all species →	zf-TRAF	TRAF-type zinc finger	Family	Interproscan
PF01344 all species →	Kelch_1	Kelch motif	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018957 all species →	Domain	Zinc finger, C3HC4 RING-type	Interproscan
IPR001293 all species →	Domain	Zinc finger, TRAF-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR037293 all species →	Homologous_superfamily	Galactose oxidase, central domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR003613 all species →	Domain	U-box domain	Interproscan
IPR006652 all species →	Repeat	Kelch repeat type 1	Interproscan
IPR013010 all species →	Domain	Zinc finger, SIAH-type	Interproscan
IPR051746 all species →	Family	Kelch domain-containing protein 8	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	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 CAB4026994.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4026994.1 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

9TPM > 0

4Conditions

13.5Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	2.99	9.09
apical branchlet · Temperature treatment at T0	6	2	1.53	4.95
apical branchlet · Temperature treatment at T25	5	2	3.23	13.54
apical branchlet · Control at T0	4	1	0.73	2.90

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	9.09
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	4.92
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.39
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.51
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
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.95
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.23
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	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
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	13.54
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.60
SRR19977425	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	2.90
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.