Gene detail

Detailed information of OS493_040278-T1 in Lophelia pertusa

Genomic Location: scaffold_1981:726...2830
NR annotation: KAJ7388031.1, Pre-mRNA-processing-splicing factor 8, partial [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
Q99PV0	Pre-mRNA-processing-splicing factor 8 OS=Mus musculus OX=10090 GN=Prpf8 PE=1 SV=2
Q6P2Q9	Pre-mRNA-processing-splicing factor 8 OS=Homo sapiens OX=9606 GN=PRPF8 PE=1 SV=2
P34369	Pre-mRNA-splicing factor 8 homolog OS=Caenorhabditis elegans OX=6239 GN=prp-8 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004404 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01398 all species →	JAB	JAB1/Mov34/MPN/PAD-1 ubiquitin protease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027652 all species →	Family	Pre-mRNA-processing-splicing factor 8	Interproscan
IPR000555 all species →	Domain	JAB1/MPN/MOV34 metalloenzyme domain	Interproscan
IPR037518 all species →	Domain	MPN domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11140 all species →	PRE-MRNA SPLICING FACTOR PRP8	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000244 all species →	Biological Process	spliceosomal tri-snRNP complex assembly	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0005682 all species →	Cellular Component	U5 snRNP	Interproscan
GO:0017070 all species →	Molecular Function	U6 snRNA binding	Interproscan
GO:0030619 all species →	Molecular Function	U1 snRNA binding	Interproscan
GO:0030620 all species →	Molecular Function	U2 snRNA binding	Interproscan
GO:0030623 all species →	Molecular Function	U5 snRNA binding	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	Interproscan
GO:0097157 all species →	Molecular Function	pre-mRNA intronic binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008233 all species →	Molecular Function	peptidase activity	Interproscan
GO:0008237 all species →	Molecular Function	metallopeptidase activity	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_040278-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_040278-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

104TPM > 0

7Conditions

33.6Max TPM

14.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	18.71	24.09
polyp at pH7 6	18	18	22.76	33.60
coral polyp · control treatment	16	16	12.11	29.22
coral polyp · oil and dispersant treatment	16	14	9.88	18.20
coral polyp · oil treatment	16	16	13.84	30.51
coral polyp · dispersant treatment	16	15	9.89	26.19
Polyp	10	7	10.14	21.43

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.09
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.19
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.98
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.46
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.36
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.31
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.18
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.91
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.68
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.38
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.01
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.66
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.65
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.87
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.50
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.21
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.60
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.30
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.76
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.83
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.48
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.04
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.55
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.39
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.40
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.16
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.08
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.22
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.61
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.61
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.71
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.32
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.27
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.60
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.30
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.78
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.99
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.23
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.68
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.42
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.27
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.91
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.37
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.89
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.46
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.56
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.25
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.01
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.82
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.27
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.85
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.78
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.17
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.57
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.51
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.42
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.65
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.09
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.73
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.66
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.42
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.04
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.38
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.73
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.71
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.19
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.16
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.83
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.34
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.27
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.63
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.30
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.90
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.62
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.27
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.46
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.43
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	19.75
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	18.45
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	14.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.90
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.00
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.