Gene detail

Detailed information of OS493_022036-T1 in Lophelia pertusa

Genomic Location: scaffold_88:966682...974354
NR annotation: KAJ7371938.1, hypothetical protein OS493_022036 [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
Q8JIR0	Polycomb complex protein BMI-1-A OS=Danio rerio OX=7955 GN=bmi1a PE=1 SV=2
Q7T3E6	Polycomb complex protein BMI-1-B OS=Danio rerio OX=7955 GN=bmi1b PE=2 SV=1
Q32KX7	Polycomb complex protein BMI-1 OS=Bos taurus OX=9913 GN=BMI1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000402 (this species only)
Ubiquitin family	ULD\|UFD\|RAWUL · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13923 all species →	zf-C3HC4_2	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF16207 all species →	RAWUL	RAWUL domain RING finger- and WD40-associated ubiquitin-like	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR032443 all species →	Domain	RAWUL domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10825 all species →	RING FINGER DOMAIN-CONTAINING, POLYCOMB GROUP COMPONENT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000122 all species →	Biological Process	negative regulation of transcription by RNA polymerase II	Interproscan
GO:0035102 all species →	Cellular Component	PRC1 complex	Interproscan
GO:1990841 all species →	Molecular Function	promoter-specific chromatin 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
K11459	PCGF4, BMI1; polycomb group RING finger protein 4	-	Chromosome and associated proteins	ko03036	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_022036-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

27.1Max TPM

5.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.57	5.01
polyp at pH7 6	18	18	3.72	7.24
coral polyp · control treatment	16	16	6.30	14.02
coral polyp · oil and dispersant treatment	16	16	7.13	18.97
coral polyp · oil treatment	16	16	5.86	8.27
coral polyp · dispersant treatment	16	16	6.69	27.13
Polyp	10	10	7.53	14.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.01
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.37
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.31
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.50
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.46
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.26
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.21
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.19
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.10
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.77
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.05
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.96
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.29
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.28
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.89
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.50
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.44
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.41
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.98
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.81
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.77
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.39
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.13
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.93
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.21
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.10
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.70
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.03
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.98
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.64
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.13
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.01
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.95
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.69
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.97
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.49
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.88
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.60
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.52
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.34
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.15
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.05
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.77
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.91
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.96
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.27
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.11
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.40
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.29
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.54
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.35
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.34
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.09
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.77
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.66
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.08
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.02
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.13
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.50
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.30
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.01
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.90
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.77
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.66
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.39
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.24
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.21
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.71
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.24
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.51
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.60
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.43
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.23
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.43
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.39
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.00

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.