Gene detail

Detailed information of OS493_023503-T1 in Lophelia pertusa

Genomic Location: scaffold_104:971422...972348
NR annotation: KAJ7384174.1, Cleavage polyadenylation factor subunit clp1 [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
A7RG82	Protein CLP1 homolog OS=Nematostella vectensis OX=45351 GN=v1g236308 PE=3 SV=1
A2VE01	Polyribonucleotide 5'-hydroxyl-kinase Clp1 OS=Bos taurus OX=9913 GN=CLP1 PE=2 SV=1
Q92989	Polyribonucleotide 5'-hydroxyl-kinase Clp1 OS=Homo sapiens OX=9606 GN=CLP1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004210 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06807 all species →	Clp1	Pre-mRNA cleavage complex II protein Clp1	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038238 all species →	Homologous_superfamily	Clp1, C-terminal domain superfamily	Interproscan
IPR045116 all species →	Family	Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3	Interproscan
IPR010655 all species →	Domain	Pre-mRNA cleavage complex subunit Clp1, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12755 all species →	CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006378 all species →	Biological Process	obsolete mRNA polyadenylation	Interproscan
GO:0006388 all species →	Biological Process	tRNA splicing, via endonucleolytic cleavage and ligation	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0051731 all species →	Molecular Function	polynucleotide 5'-hydroxyl-kinase activity	Interproscan
GO:0031124 all species →	Biological Process	mRNA 3'-end processing	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_023503-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_023503-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

102TPM > 0

7Conditions

50.3Max TPM

7.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	4.49	9.75
polyp at pH7 6	18	13	4.77	9.39
coral polyp · control treatment	16	16	12.89	50.32
coral polyp · oil and dispersant treatment	16	16	9.79	43.38
coral polyp · oil treatment	16	16	10.37	16.62
coral polyp · dispersant treatment	16	15	6.26	14.66
Polyp	10	10	7.07	12.68

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	-	9.75
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.35
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.44
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.08
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.73
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.69
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.61
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.48
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.85
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.91
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.04
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.39
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.09
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.91
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.58
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.41
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.34
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.92
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.65
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.44
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.06
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.35
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	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
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.32
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.52
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.35
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.67
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.87
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.68
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.13
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.06
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.60
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.56
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.86
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.74
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.38
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.15
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.93
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.82
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.80
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.65
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.60
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.05
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.11
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.91
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.63
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.29
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.33
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.26
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.62
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.22
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.37
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.91
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.59
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.08
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.41
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.04
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.57
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.44
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.89
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.68
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.66
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.17
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.84
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.52
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.40
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.40
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.17
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.07
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.73
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.67
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.08
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.21
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.81
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.20
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.44
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.68
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.52
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.69

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.