Gene detail

Detailed information of OS493_024749-T1 in Lophelia pertusa

Genomic Location: scaffold_117:492581...499579
NR annotation: KAJ7378086.1, RNA endoribonuclease [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
Q5T5J6	Transcriptional protein SWT1 OS=Homo sapiens OX=9606 GN=SWT1 PE=1 SV=1
Q9DBQ9	Transcriptional protein SWT1 OS=Mus musculus OX=10090 GN=Swt1 PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004303 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13638 all species →	PIN_4	PIN domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001202 all species →	Domain	WW domain	Interproscan
IPR036020 all species →	Homologous_superfamily	WW domain superfamily	Interproscan
IPR002716 all species →	Domain	PIN domain	Interproscan
IPR052626 all species →	Family	SWT1 Transcriptional Regulator	Interproscan
IPR029060 all species →	Homologous_superfamily	PIN-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16161 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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_024749-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_024749-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

108TPM > 0

7Conditions

15.3Max TPM

3.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.89	5.31
polyp at pH7 6	18	17	3.28	5.21
coral polyp · control treatment	16	16	4.06	13.03
coral polyp · oil and dispersant treatment	16	16	2.49	15.27
coral polyp · oil treatment	16	16	2.95	6.38
coral polyp · dispersant treatment	16	15	2.83	6.31
Polyp	10	10	2.04	4.48

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.16
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.04
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.31
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.17
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.16
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.71
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.61
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.38
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.08
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.94
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.75
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.93
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.73
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.68
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.48
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.34
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.92
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.70
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.30
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.17
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.12
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.03
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.15
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.77
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.73
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.50
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.43
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.72
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.70
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.79
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.05
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.65
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.91
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.76
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.90
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.77
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.68
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.33
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.38
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.37
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.79
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.21
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.11
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.39
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.01
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.71
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.31
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.17
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.34
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.73
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.40
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.99
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.99
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.54
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.24
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.67
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.26
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.99
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.17
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.07
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.55

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.