Gene detail

Detailed information of OS493_015427-T1 in Lophelia pertusa

Genomic Location: scaffold_46:1685097...1687531
NR annotation: KAJ7372962.1, Protein patched 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
Q98864	Protein patched homolog 1 OS=Danio rerio OX=7955 GN=ptch1 PE=2 SV=1
O35595	Protein patched homolog 2 OS=Mus musculus OX=10090 GN=Ptch2 PE=2 SV=2
Q61115	Protein patched homolog 1 OS=Mus musculus OX=10090 GN=Ptch1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002045 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12349 all species →	Sterol-sensing	Sterol-sensing domain of SREBP cleavage-activation	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000731 all species →	Domain	Sterol-sensing domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46022 all species →	PROTEIN PATCHED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005119 all species →	Molecular Function	smoothened binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008158 all species →	Molecular Function	hedgehog receptor activity	Interproscan
GO:0045879 all species →	Biological Process	negative regulation of smoothened signaling pathway	Interproscan
GO:0097108 all species →	Molecular Function	hedgehog family protein binding	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_015427-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_015427-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

93TPM > 0

7Conditions

20.4Max TPM

4.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	2.68	7.92
polyp at pH7 6	18	10	1.85	6.25
coral polyp · control treatment	16	16	5.89	20.44
coral polyp · oil and dispersant treatment	16	15	7.10	18.33
coral polyp · oil treatment	16	16	3.93	10.55
coral polyp · dispersant treatment	16	14	5.90	11.45
Polyp	10	9	1.37	2.36

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.92
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.75
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.26
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.56
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.72
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.61
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.05
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.06
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.90
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.87
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.74
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.70
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.26
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.22
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.98
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.29
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.44
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.30
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.82
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.96
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.22
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.76
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.40
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.70
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.63
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.90
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.78
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.33
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.57
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.57
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.62
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.99
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.18
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.54
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.24
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.57
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.28
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.68
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.27
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.18
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.08
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.86
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.89
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.70
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.20
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.24
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.45
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.30
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.81
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.16
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.57
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.34
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.53
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.32
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.04
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.43
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.36
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.04
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.52
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.10
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.04
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.95
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.