Gene detail

Detailed information of OS493_012055-T1 in Lophelia pertusa

Genomic Location: scaffold_31:1299452...1306696
NR annotation: KAJ7392393.1, E3 ubiquitin-protein transferase rmnd5a [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q640V2	E3 ubiquitin-protein ligase RMND5A OS=Xenopus tropicalis OX=8364 GN=rmnd5a PE=2 SV=1
Q9H871	E3 ubiquitin-protein transferase RMND5A OS=Homo sapiens OX=9606 GN=RMND5A PE=1 SV=1
Q80YQ8	E3 ubiquitin-protein ligase RMND5A OS=Mus musculus OX=10090 GN=Rmnd5a PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006710 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13445 all species →	zf-RING_UBOX	RING-type zinc-finger	Domain	Interproscan
PF10607 all species →	CTLH	CTLH/CRA C-terminal to LisH motif domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013144 all species →	Domain	CRA domain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR006595 all species →	Domain	CTLH, C-terminal LisH motif	Interproscan
IPR027370 all species →	Domain	Zinc finger, RING-type, eukaryotic	Interproscan
IPR024964 all species →	Domain	CTLH/CRA C-terminal to LisH motif domain	Interproscan
IPR044063 all species →	Domain	Gid-type RING finger domain	Interproscan
IPR045098 all species →	Family	Fyv10 family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12170 all species →	MACROPHAGE ERYTHROBLAST ATTACHER-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0034657 all species →	Cellular Component	GID complex	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	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
K23333	RMND5; E3 ubiquitin-protein transferase RMND5	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 OS493_012055-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples

110TPM > 0

7Conditions

30.7Max TPM

12.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.09	13.44
polyp at pH7 6	18	18	9.19	13.00
coral polyp · control treatment	16	16	15.64	30.74
coral polyp · oil and dispersant treatment	16	16	15.15	23.34
coral polyp · oil treatment	16	16	12.20	16.29
coral polyp · dispersant treatment	16	16	12.24	19.10
Polyp	10	10	9.47	19.39

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.44
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.80
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.18
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.95
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.92
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.20
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.60
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.17
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.05
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.53
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.96
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.84
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.45
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.57
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.46
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.38
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.98
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.92
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.91
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.85
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.65
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.82
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.60
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.74
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.58
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.90
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.88
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.45
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.41
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.84
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.22
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.13
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.30
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.09
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.93
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.34
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.51
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.66
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.37
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.93
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.52
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.39
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.48
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.77
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.39
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.13
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.72
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.29
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.97
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.73
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.44
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.07
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.83
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.54
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.24
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.81
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.38
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.89
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.02
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.27
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.10
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.68
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.49
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.91
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.62
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.74
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.68
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.50
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.38
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.39
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.67
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.57
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.39
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.28
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.10
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.91
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.34

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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.