Gene detail

Detailed information of OS493_039583-T1 in Lophelia pertusa

Genomic Location: scaffold_1278:12142...16962
NR annotation: KAJ7312658.1, putative E3 ubiquitin-protein ligase herc1 [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
Q15751	Probable E3 ubiquitin-protein ligase HERC1 OS=Homo sapiens OX=9606 GN=HERC1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006628 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00415 all species →	RCC1	Regulator of chromosome condensation (RCC1) repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051553 all species →	Family	Ran GTPase-activating	Interproscan
IPR009091 all species →	Homologous_superfamily	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Interproscan
IPR000408 all species →	Repeat	Regulator of chromosome condensation, RCC1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45982 all species →	REGULATOR OF CHROMOSOME CONDENSATION	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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_039583-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_039583-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

69TPM > 0

7Conditions

5.4Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	2.21	5.37
polyp at pH7 6	18	9	1.74	5.39
coral polyp · control treatment	16	14	2.10	4.38
coral polyp · oil and dispersant treatment	16	11	0.99	3.69
coral polyp · oil treatment	16	9	1.68	4.99
coral polyp · dispersant treatment	16	9	0.90	3.60
Polyp	10	6	1.07	2.53

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.37
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.30
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.91
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.54
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.39
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.85
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.78
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.60
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.41
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.83
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.35
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.38
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.74
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.73
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.47
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.22
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.91
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.59
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.55
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.54
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.69
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.19
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.79
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.88
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.78
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.71
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.99
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.31
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.08
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.34
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.14
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.85
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.60
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.64
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.44
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.53
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.80
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.78
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.45
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.10
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.