Gene detail

Detailed information of OS493_020269-T1 in Lophelia pertusa

Genomic Location: scaffold_74:806471...820872
NR annotation: KAJ7384688.1, SNW domain-containing protein 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
Q5R7R9	SNW domain-containing protein 1 OS=Pongo abelii OX=9601 GN=SNW1 PE=2 SV=1
Q13573	SNW domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SNW1 PE=1 SV=1
Q1JQE0	SNW domain-containing protein 1 OS=Bos taurus OX=9913 GN=SNW1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007118 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02731 all species →	SKIP_SNW	SKIP/SNW domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017862 all species →	Family	SKI-interacting protein, SKIP	Interproscan
IPR004015 all species →	Domain	SKI-interacting protein SKIP, SNW domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12096 all species →	NUCLEAR PROTEIN SKIP-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	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
K06063	SNW1, SKIIP, SKIP; SNW domain-containing protein 1	-	Spliceosome	ko03041	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_020269-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

38.3Max TPM

22.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	18.96	28.44
polyp at pH7 6	18	18	18.61	25.25
coral polyp · control treatment	16	16	26.77	36.44
coral polyp · oil and dispersant treatment	16	16	27.39	38.35
coral polyp · oil treatment	16	16	23.87	30.86
coral polyp · dispersant treatment	16	16	18.76	27.36
Polyp	10	10	20.73	34.37

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.44
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.68
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.67
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.33
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.15
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.00
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.46
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.10
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.06
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.48
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.07
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.37
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.93
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.25
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.67
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.31
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.31
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.74
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.61
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.51
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.82
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.74
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.96
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.48
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.51
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.21
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.44
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.92
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.18
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.23
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.96
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.49
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.27
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.90
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.59
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.33
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.50
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.35
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.08
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.97
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.41
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.33
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.68
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.82
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.54
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.46
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.30
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.17
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.97
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.25
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.25
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.86
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.16
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.79
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.87
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.09
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.73
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.18
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.02
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.98
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.91
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.27
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.54
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.36
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.86
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.57
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.71
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.61
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.45
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.14
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.18
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.06
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.35
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.98
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.94
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.93
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	34.37
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.64
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	23.84
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.47
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	21.33
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	21.01
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.78
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	15.37
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.71
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.76

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.