Gene detail

Detailed information of OS493_023505-T1 in Lophelia pertusa

Genomic Location: scaffold_104:977950...981988
NR annotation: KAJ7384176.1, 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
PF16573 all species →	CLP1_N	N-terminal beta-sandwich domain of polyadenylation factor	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR032324 all species →	Domain	Clp1, N-terminal beta-sandwich domain	Interproscan
IPR038239 all species →	Homologous_superfamily	Clp1, N-terminal beta-sandwich domain superfamily	Interproscan

PANTHER

No PANTHER signature was detected for OS493_023505-T1. This gene does have a gene model — the search simply returned no hit.

Gene Ontology

No Gene Ontology signature was detected for OS493_023505-T1. This gene does have a gene model — the search simply returned no hit.

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_023505-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_023505-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

96TPM > 0

7Conditions

32.0Max TPM

3.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	2.28	7.11
polyp at pH7 6	18	9	1.31	4.86
coral polyp · control treatment	16	16	5.48	31.96
coral polyp · oil and dispersant treatment	16	16	4.80	29.52
coral polyp · oil treatment	16	16	2.95	5.20
coral polyp · dispersant treatment	16	15	3.20	7.80
Polyp	10	9	2.53	4.52

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.11
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.33
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.20
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.89
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.31
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.23
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.62
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.59
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.16
SRR11359495	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
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.86
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.12
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.57
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.70
SRR11359500	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
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359515	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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.96
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.86
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.16
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.07
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.04
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.00
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.93
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.70
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.26
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.19
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.17
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.52
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.49
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.97
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.25
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.21
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.24
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.12
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.09
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.76
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.37
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.00
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.98
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.19
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.03
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.81
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.61
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.27
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.85
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.32
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.80
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.62
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.55
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.83
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.01
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.64
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.50
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.49
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.52
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.90
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.44
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.48
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.27
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.33
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.93
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.