Gene detail

Detailed information of OS493_015426-T1 in Lophelia pertusa

Genomic Location: scaffold_46:1673870...1678852
NR annotation: KAJ7372961.1, 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
Q61115	Protein patched homolog 1 OS=Mus musculus OX=10090 GN=Ptch1 PE=1 SV=1
Q13635	Protein patched homolog 1 OS=Homo sapiens OX=9606 GN=PTCH1 PE=1 SV=2

Gene family

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

Pfam domain

No Pfam domain signature was detected for OS493_015426-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

No InterPro signature was detected for OS493_015426-T1. This gene does have a gene model — the search simply returned no hit.

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_015426-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_015426-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

89TPM > 0

7Conditions

17.7Max TPM

3.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	1.39	4.26
polyp at pH7 6	18	10	1.60	3.83
coral polyp · control treatment	16	16	4.35	17.71
coral polyp · oil and dispersant treatment	16	15	5.79	13.05
coral polyp · oil treatment	16	16	3.46	9.35
coral polyp · dispersant treatment	16	14	5.34	13.00
Polyp	10	7	0.70	1.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.26
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.40
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.20
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.75
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.68
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.23
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
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
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.74
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.45
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.99
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.55
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.42
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.30
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.42
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	17.71
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.10
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.58
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.67
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.21
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.55
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.51
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.84
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.15
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.46
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.05
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.58
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.50
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.39
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.40
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.12
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.01
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.12
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.64
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.48
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.08
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.92
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.24
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.14
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.38
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.38
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.54
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.37
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.46
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.00
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.98
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.70
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.28
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.86
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.64
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.16
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.44
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.90
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.70
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
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	-	1.72
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.14
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.05
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.79
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.62
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.53
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	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.