Gene detail

Detailed information of OS493_006324-T1 in Lophelia pertusa

Genomic Location: scaffold_13:2025778...2036971
NR annotation: KAJ7393353.1, cleavage stimulation factor, 3' pre-RNA, subunit 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)

UniProt accession	Description
Q05048	Cleavage stimulation factor subunit 1 OS=Homo sapiens OX=9606 GN=CSTF1 PE=1 SV=1
Q99LC2	Cleavage stimulation factor subunit 1 OS=Mus musculus OX=10090 GN=Cstf1 PE=1 SV=1
Q5R8K2	Cleavage stimulation factor subunit 1 OS=Pongo abelii OX=9601 GN=CSTF1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002738 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16699 all species →	CSTF1_dimer	Cleavage stimulation factor subunit 1, dimerisation domain	Domain	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR044633 all species →	Family	Cleavage stimulation factor subunit 1-like	Interproscan
IPR032028 all species →	Domain	Cleavage stimulation factor subunit 1, dimerisation domain	Interproscan
IPR038184 all species →	Homologous_superfamily	CSTF1, dimerization domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44133 all species →	CLEAVAGE STIMULATION FACTOR SUBUNIT 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005848 all species →	Cellular Component	mRNA cleavage stimulating factor complex	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_006324-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_006324-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

109TPM > 0

7Conditions

28.8Max TPM

11.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.26	13.06
polyp at pH7 6	18	17	8.01	12.40
coral polyp · control treatment	16	16	16.00	28.55
coral polyp · oil and dispersant treatment	16	16	13.93	28.78
coral polyp · oil treatment	16	16	14.77	19.78
coral polyp · dispersant treatment	16	16	11.66	20.40
Polyp	10	10	9.80	26.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.06
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.55
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.48
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.56
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.58
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.10
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.05
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.78
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.65
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.36
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.31
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.03
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.71
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.66
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.50
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.40
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.74
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.38
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.34
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.78
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.51
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.49
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.41
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.39
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.92
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.54
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.25
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.21
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.76
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.58
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.55
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.81
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.28
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.68
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.71
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.96
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.48
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.34
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.17
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.58
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.54
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.78
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.92
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.94
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.88
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.68
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.56
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.63
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.59
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.55
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.44
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.82
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.09
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.80
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.41
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.57
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.45
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.35
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.93
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.90
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.84
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.34
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.45
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.40
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.40
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.38
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.74
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.27
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.70
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.21
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.35
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.51
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.37
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.71
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.20
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.05
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.21
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	26.33
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.08
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.49
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.97
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.97
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.53
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.77

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.