Gene detail

Detailed information of OS493_022862-T1 in Lophelia pertusa

Genomic Location: scaffold_98:301392...318457
NR annotation: KAJ7384232.1, hypothetical protein OS493_022862 [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
P98165	Very low-density lipoprotein receptor OS=Gallus gallus OX=9031 GN=VLDLR PE=1 SV=1
Q700K0	SCO-spondin OS=Rattus norvegicus OX=10116 GN=Sspo PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000956 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00057 all species →	Ldl_recept_a	Low-density lipoprotein receptor domain class A	Repeat	Interproscan
PF00041 all species →	fn3	Fibronectin type III domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036055 all species →	Homologous_superfamily	LDL receptor-like superfamily	Interproscan
IPR002172 all species →	Repeat	Low-density lipoprotein (LDL) receptor class A repeat	Interproscan
IPR050685 all species →	Family	Low-density lipoprotein receptor	Interproscan
IPR003961 all species →	Domain	Fibronectin type III	Interproscan
IPR036116 all species →	Homologous_superfamily	Fibronectin type III superfamily	Interproscan
IPR023415 all species →	Conserved_site	Low-density lipoprotein (LDL) receptor class A, conserved site	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24270 all species →	LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma 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_022862-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_022862-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

32.7Max TPM

10.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.74	19.26
polyp at pH7 6	18	17	10.93	22.44
coral polyp · control treatment	16	16	11.14	28.47
coral polyp · oil and dispersant treatment	16	15	16.22	32.71
coral polyp · oil treatment	16	16	8.34	16.34
coral polyp · dispersant treatment	16	16	12.59	28.77
Polyp	10	10	3.00	6.04

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	-	19.26
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.73
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.59
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.56
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.56
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.51
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.99
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.86
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.43
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.74
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.77
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.77
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.45
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.51
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.09
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.44
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.82
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.81
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.66
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.16
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.47
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.33
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.82
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.64
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.58
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.30
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.37
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.85
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.73
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.63
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.54
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.70
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.42
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.23
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.83
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.83
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.41
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.68
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.71
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.43
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.99
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.75
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.55
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.22
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.12
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.23
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.46
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.34
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.17
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.68
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.94
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.85
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.21
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.57
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.78
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.45
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.42
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.87
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.17
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.91
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.77
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.21
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.77
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.35
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.86
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.98
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.24
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.41
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.35
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.97
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.83
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.25
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.03
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.31
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.04
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.77
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.58
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.14
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.56
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.72
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.47
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.69

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.