Gene detail

Detailed information of OS493_004120-T1 in Lophelia pertusa

Genomic Location: scaffold_8:2541514...2555621
NR annotation: KAJ7387154.1, Pre-mRNA-processing factor 19 [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
Q08E38	Pre-mRNA-processing factor 19 OS=Bos taurus OX=9913 GN=PRPF19 PE=2 SV=1
Q99KP6	Pre-mRNA-processing factor 19 OS=Mus musculus OX=10090 GN=Prpf19 PE=1 SV=1
Q9JMJ4	Pre-mRNA-processing factor 19 OS=Rattus norvegicus OX=10116 GN=Prpf19 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007086 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|U-box · 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
PF08606 all species →	Prp19	Prp19/Pso4-like	Domain	Interproscan
PF04564 all species →	U-box	U-box 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
IPR038959 all species →	Family	Pre-mRNA-processing factor 19	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR003613 all species →	Domain	U-box domain	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR013915 all species →	Domain	Pre-mRNA-splicing factor 19	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43995 all species →	PRE-MRNA-PROCESSING FACTOR 19	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000974 all species →	Cellular Component	Prp19 complex	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0071006 all species →	Cellular Component	U2-type catalytic step 1 spliceosome	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	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
K10599	PRPF19, PRP19; pre-mRNA-processing factor 19	EC:2.3.2.27	DNA repair and recombination proteins	ko03400	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_004120-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

51.2Max TPM

20.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	20.35	28.38
polyp at pH7 6	18	18	21.78	29.48
coral polyp · control treatment	16	16	24.91	37.69
coral polyp · oil and dispersant treatment	16	16	19.18	32.57
coral polyp · oil treatment	16	16	21.09	42.44
coral polyp · dispersant treatment	16	16	16.72	38.97
Polyp	10	10	22.46	51.23

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	-	28.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.74
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.42
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.72
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.96
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.35
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.30
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.86
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.73
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.16
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.81
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.05
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.82
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.66
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.48
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.95
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.89
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.16
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.67
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.63
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.32
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.91
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.16
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.43
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.08
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.95
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.56
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.67
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.70
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.69
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.36
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.99
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.85
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.38
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.95
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.62
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.87
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.89
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.64
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.15
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.57
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.13
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.48
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.35
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.43
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.14
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.51
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.39
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.49
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.34
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.68
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.15
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.57
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.57
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.59
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.57
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.94
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.27
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.17
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.90
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.97
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.09
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.19
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.83
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.23
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.42
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.30
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.02
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.98
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.28
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.50
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.52
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.02
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.76
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	51.23
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	24.40
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	23.82
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	22.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.65
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	21.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	16.23
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.54

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.