Gene detail

Detailed information of OS493_014655-T1 in Lophelia pertusa

Genomic Location: scaffold_42:335424...356938
NR annotation: KAJ7334345.1, E3 ubiquitin-protein ligase lrsam1 [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
Q6UWE0	E3 ubiquitin-protein ligase LRSAM1 OS=Homo sapiens OX=9606 GN=LRSAM1 PE=1 SV=1
Q80ZI6	E3 ubiquitin-protein ligase LRSAM1 OS=Mus musculus OX=10090 GN=Lrsam1 PE=1 SV=1
Q5M7X9	Mitochondrial ubiquitin ligase activator of nfkb 1-A OS=Danio rerio OX=7955 GN=mul1a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003925 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13920 all species →	zf-C3HC4_3	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF00536 all species →	SAM_1	SAM domain (Sterile alpha motif)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013761 all species →	Homologous_superfamily	Sterile alpha motif/pointed domain superfamily	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR051728 all species →	Family	RING-FYVE domain-containing E3 ubiquitin-protein ligase	Interproscan
IPR001660 all species →	Domain	Sterile alpha motif domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14879 all species →	CASPASE REGULATOR, RING FINGER DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein 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 OS493_014655-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_014655-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

75.0Max TPM

29.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.82	34.32
polyp at pH7 6	18	18	21.10	32.87
coral polyp · control treatment	16	16	34.52	60.85
coral polyp · oil and dispersant treatment	16	16	47.59	69.01
coral polyp · oil treatment	16	16	29.35	40.65
coral polyp · dispersant treatment	16	16	32.57	74.97
Polyp	10	10	23.85	46.30

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.51
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.49
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.13
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.99
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.71
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.35
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.58
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.06
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.99
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.67
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.34
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.16
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.83
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.76
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.83
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.87
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.75
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.36
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.78
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.06
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.53
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.93
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.50
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.97
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.27
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.08
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.44
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.43
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.93
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.24
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.85
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.47
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.70
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.53
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.04
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.43
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.98
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.99
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.70
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.01
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.20
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.67
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.62
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.41
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.16
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.24
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.25
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.42
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.13
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.50
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.74
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.65
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.48
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.37
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.97
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.71
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.48
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.32
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.98
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.92
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.84
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.43
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.97
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.53
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.85
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.29
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.52
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.81
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.45
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.35
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.41
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.84
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.83
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	46.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	39.68
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	30.84
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	26.24
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	24.03
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	20.47
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.41
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.12
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.99
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.45

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.