Gene detail

Detailed information of CAB3992156.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3992156.1, E3 ubiquitin- ligase UBR5 isoform X2 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3992156.1 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
Q80TP3	E3 ubiquitin-protein ligase UBR5 OS=Mus musculus OX=10090 GN=Ubr5 PE=1 SV=2
O95071	E3 ubiquitin-protein ligase UBR5 OS=Homo sapiens OX=9606 GN=UBR5 PE=1 SV=2
Q62671	E3 ubiquitin-protein ligase UBR5 OS=Rattus norvegicus OX=10116 GN=Ubr5 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002381 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00658 all species →	PABP	Poly-adenylate binding protein, unique domain	Family	Interproscan
PF00632 all species →	HECT	HECT-domain (ubiquitin-transferase)	Domain	Interproscan
PF11547 all species →	E3_UbLigase_EDD	E3 ubiquitin ligase EDD	Domain	Interproscan
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000569 all species →	Domain	HECT domain	Interproscan
IPR003126 all species →	Domain	Zinc finger, UBR-type	Interproscan
IPR002004 all species →	Domain	Polyadenylate-binding protein/Hyperplastic disc protein	Interproscan
IPR008351 all species →	Family	Mitogen-activated protein (MAP) kinase, JNK	Interproscan
IPR024725 all species →	Domain	E3 ubiquitin-protein ligase UBR5, ubiquitin-associated domain	Interproscan
IPR009091 all species →	Homologous_superfamily	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Interproscan
IPR047503 all species →	Domain	E3 ubiquitin-protein ligase UBR5, UBR-box	Interproscan
IPR036053 all species →	Homologous_superfamily	PABC (PABP) domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR035983 all species →	Homologous_superfamily	HECT, E3 ligase catalytic domain	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46276 all species →	E3 UBIQUITIN-PROTEIN LIGASE UBR5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004707 all species →	Molecular Function	MAP kinase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0034450 all species →	Molecular Function	ubiquitin-ubiquitin ligase activity	Interproscan
GO:0090263 all species →	Biological Process	positive regulation of canonical Wnt signaling pathway	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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
K10593	EDD1, UBR5; E3 ubiquitin-protein ligase EDD1	EC:2.3.2.26	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 CAB3992156.1 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

19TPM > 0

4Conditions

62.4Max TPM

14.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	24.42	62.40
apical branchlet · Temperature treatment at T0	6	6	16.96	38.08
apical branchlet · Temperature treatment at T25	5	4	7.33	14.97
apical branchlet · Control at T0	4	3	4.48	10.70

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	62.40
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	23.44
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	20.60
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	19.03
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.58
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	9.49
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	38.08
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	33.66
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.41
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.27
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.38
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.98
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	14.97
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.41
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.01
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	5.28
SRR19977434	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	10.70
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	6.26
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.97
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.