Gene detail

Detailed information of OS493_009614-T1 in Lophelia pertusa

Genomic Location: scaffold_23:758482...767640
NR annotation: KAJ7363460.1, Cleavage stimulation factor subunit 2 [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
Q8BIQ5	Cleavage stimulation factor subunit 2 OS=Mus musculus OX=10090 GN=Cstf2 PE=1 SV=2
P33240	Cleavage stimulation factor subunit 2 OS=Homo sapiens OX=9606 GN=CSTF2 PE=1 SV=1
Q5RDA3	Cleavage stimulation factor subunit 2 OS=Pongo abelii OX=9601 GN=CSTF2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006395 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF14304 all species →	CSTF_C	Transcription termination and cleavage factor C-terminal	Domain	Interproscan
PF14327 all species →	CSTF2_hinge	Hinge domain of cleavage stimulation factor subunit 2	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR038192 all species →	Homologous_superfamily	Transcription termination and cleavage factor, C-terminal domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR026896 all species →	Domain	Transcription termination and cleavage factor, C-terminal domain	Interproscan
IPR025742 all species →	Domain	Cleavage stimulation factor subunit 2, hinge domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45735 all species →	CLEAVAGE STIMULATION FACTOR SUBUNIT 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005847 all species →	Cellular Component	mRNA cleavage and polyadenylation specificity factor complex	Interproscan
GO:0098789 all species →	Biological Process	obsolete pre-mRNA cleavage required for polyadenylation	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14407	CSTF2, RNA15; cleavage stimulation factor subunit 2	-	Messenger RNA biogenesis	ko03019	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_009614-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

47.8Max TPM

23.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.26	41.14
polyp at pH7 6	18	18	28.97	47.71
coral polyp · control treatment	16	16	23.67	39.02
coral polyp · oil and dispersant treatment	16	16	20.68	43.31
coral polyp · oil treatment	16	16	20.74	29.66
coral polyp · dispersant treatment	16	16	14.01	23.88
Polyp	10	10	28.21	47.83

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.14
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.83
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.62
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.90
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.30
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.07
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.86
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.89
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.11
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.00
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.68
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.08
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.71
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.48
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.64
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.71
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.75
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.96
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.02
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.81
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.23
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.62
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.35
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.41
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.02
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.36
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.33
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.57
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.95
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.36
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.93
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.84
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.20
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.82
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.40
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.17
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.31
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.04
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.50
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.07
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.02
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.73
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.54
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.85
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.66
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.52
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.10
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.68
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.03
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.66
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.16
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.76
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.82
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.28
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.86
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.17
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.15
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.27
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.28
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.88
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.83
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.60
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.29
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.11
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.89
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.58
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.12
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.53
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.76
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.13
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.55
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.82
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.43
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	47.83
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	36.85
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	34.02
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	33.09
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	27.39
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	26.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	24.64
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	21.34
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	18.72
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.25

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.