Gene detail

Detailed information of CAB3993112.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3993112.1, E3 ubiquitin- ligase UBR4, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3993112.1 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
A2AN08	E3 ubiquitin-protein ligase UBR4 OS=Mus musculus OX=10090 GN=Ubr4 PE=1 SV=1
Q5T4S7	E3 ubiquitin-protein ligase UBR4 OS=Homo sapiens OX=9606 GN=UBR4 PE=1 SV=1
Q2TL32	E3 ubiquitin-protein ligase UBR4 OS=Rattus norvegicus OX=10116 GN=Ubr4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001776 (this species only)
Ubiquitin family	E3\|E3 activity\|UBR-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF19423 all species →	E3_UBR4_N	E3 ubiquitin-protein ligase UBR4 N-terminal	Domain	Interproscan
PF02207 all species →	zf-UBR	Putative zinc finger in N-recognin (UBR box)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045841 all species →	Domain	E3 ubiquitin-protein ligase UBR4, N-terminal	Interproscan
IPR003126 all species →	Domain	Zinc finger, UBR-type	Interproscan
IPR003903 all species →	Conserved_site	Ubiquitin interacting motif	Interproscan
IPR047509 all species →	Domain	E3 ubiquitin-protein ligase UBR4-like, UBR-box	Interproscan
IPR045189 all species →	Family	E3 ubiquitin ligase UBR4-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21725 all species →	E3 UBIQUITIN-PROTEIN LIGASE UBR4	Interproscan

Gene Ontology

GO term	Category	Description	Source
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

No KEGG orthology assignment for CAB3993112.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3993112.1 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

14TPM > 0

4Conditions

6.1Max TPM

2.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	2.04	5.37
apical branchlet · Temperature treatment at T0	6	4	1.92	5.05
apical branchlet · Temperature treatment at T25	5	2	1.85	6.10
apical branchlet · Control at T0	4	3	2.55	4.71

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	5.37
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.35
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.30
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.82
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.38
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.05
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.49
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.58
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.37
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
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	6.10
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	3.14
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	4.71
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	3.16
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	2.33
SRR19977445	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.