Gene detail

Detailed information of OS493_018738-T1 in Lophelia pertusa

Genomic Location: scaffold_62:1772640...1773865
NR annotation: KAJ7385044.1, Retinoblastoma-like protein 1 [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004666 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08934 all species →	Rb_C	Rb C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015030 all species →	Domain	Retinoblastoma-associated protein, C-terminal	Interproscan
IPR028309 all species →	Family	Retinoblastoma protein family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13742 all species →	RETINOBLASTOMA-ASSOCIATED PROTEIN RB -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0051726 all species →	Biological Process	regulation of cell cycle	Interproscan
GO:2000134 all species →	Biological Process	negative regulation of G1/S transition of mitotic cell cycle	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_018738-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_018738-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

108TPM > 0

7Conditions

41.6Max TPM

17.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.65	37.38
polyp at pH7 6	18	17	22.26	32.15
coral polyp · control treatment	16	16	18.47	36.89
coral polyp · oil and dispersant treatment	16	16	11.60	41.65
coral polyp · oil treatment	16	16	14.38	30.60
coral polyp · dispersant treatment	16	16	17.27	39.33
Polyp	10	9	11.16	24.04

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.38
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.31
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.54
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.65
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.37
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.74
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.37
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.15
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.83
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.52
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.88
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.79
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.30
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.87
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.09
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.69
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.39
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.15
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.37
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.78
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.16
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.28
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.53
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.27
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.73
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.36
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.33
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.32
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.07
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.89
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.36
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.88
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.64
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.10
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.47
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.02
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.80
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.13
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.01
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.59
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.65
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.49
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.99
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.88
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.52
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.36
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.21
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.37
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.56
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.09
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.89
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.83
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.42
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.10
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.53
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.84
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.30
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.78
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.49
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.43
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.68
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.33
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.61
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.71
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.55
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.98
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.79
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.98
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.91
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.35
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.33
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.02
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.65
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.37
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.04
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	23.14
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.90
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.04
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.48
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.45
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.14
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.