Gene detail

Detailed information of OS493_015428-T1 in Lophelia pertusa

Genomic Location: scaffold_46:1687729...1697721
NR annotation: KAJ7372963.1, 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
Q90693	Protein patched homolog 1 OS=Gallus gallus OX=9031 GN=PTCH1 PE=1 SV=1
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

Gene family

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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02460 all species →	Patched	Patched family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003392 all species →	Family	Protein patched/dispatched	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
GO:0016020 all species →	Cellular Component	membrane	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_015428-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_015428-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

29.3Max TPM

7.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.21	8.05
polyp at pH7 6	18	18	5.36	7.63
coral polyp · control treatment	16	16	8.01	24.08
coral polyp · oil and dispersant treatment	16	16	11.21	29.28
coral polyp · oil treatment	16	16	7.55	14.29
coral polyp · dispersant treatment	16	16	8.53	21.14
Polyp	10	10	3.32	7.58

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	-	8.05
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.03
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.99
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.66
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.11
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.08
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.45
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.31
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.27
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.08
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.84
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.89
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.21
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.17
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.97
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.50
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.42
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.16
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.42
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.24
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.59
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.08
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.20
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.59
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.20
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.85
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.64
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.63
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.45
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.71
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.66
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.44
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.59
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.28
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.79
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.97
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.07
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.19
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.79
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.05
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.71
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.24
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.10
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.38
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.13
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.17
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.57
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.83
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.43
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.03
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.96
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.73
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.72
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.60
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.40
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.03
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.14
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.73
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.54
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.06
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.59
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.44
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.39
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.65
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.25
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.22
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.21
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.14
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.79
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.32
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.84
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.36
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.35
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.31
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.37
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.31

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.