Gene detail

Detailed information of OS493_025908-T1 in Lophelia pertusa

Genomic Location: scaffold_130:949337...952432
NR annotation: KAJ7371439.1, Hyaluronan and proteoglycan link protein 3 [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
P03994	Hyaluronan and proteoglycan link protein 1 OS=Rattus norvegicus OX=10116 GN=Hapln1 PE=1 SV=2
Q9QUP5	Hyaluronan and proteoglycan link protein 1 OS=Mus musculus OX=10090 GN=Hapln1 PE=1 SV=1
P16112	Aggrecan core protein OS=Homo sapiens OX=9606 GN=ACAN PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001789 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00008 all species →	EGF	EGF-like domain	Domain	Interproscan
PF00193 all species →	Xlink	Extracellular link domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR016186 all species →	Homologous_superfamily	C-type lectin-like/link domain superfamily	Interproscan
IPR003609 all species →	Domain	PAN/Apple domain	Interproscan
IPR000538 all species →	Domain	Link domain	Interproscan
IPR016187 all species →	Homologous_superfamily	C-type lectin fold	Interproscan
IPR043210 all species →	Family	CD44 antigen-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10225 all species →	HYALURONAN RECEPTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005540 all species →	Molecular Function	hyaluronic acid binding	Interproscan
GO:0007155 all species →	Biological Process	cell adhesion	Interproscan
GO:0004888 all species →	Molecular Function	transmembrane signaling receptor activity	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K06851	HAPLN2; hyaluronan and proteoglycan link protein 2	-	Glycosaminoglycan binding proteins	ko00536	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_025908-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

55TPM > 0

7Conditions

5.1Max TPM

0.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	5	0.26	1.41
polyp at pH7 6	18	5	0.19	0.89
coral polyp · control treatment	16	12	0.48	1.40
coral polyp · oil and dispersant treatment	16	8	0.20	0.62
coral polyp · oil treatment	16	9	0.30	1.27
coral polyp · dispersant treatment	16	9	0.26	1.02
Polyp	10	7	1.36	5.13

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	-	1.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.38
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.69
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.51
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
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	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
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
SRR11359518	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
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.89
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.86
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.56
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.54
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.53
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
SRR11359502	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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359515	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
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.40
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.97
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.94
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.87
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.86
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.73
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.49
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.26
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.19
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.10
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.62
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.56
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.07
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.27
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.71
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.56
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.53
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.34
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.29
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.20
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.54
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.50
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.18
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705969	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
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.13
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.04
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.85
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.67
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.31
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.12
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.47
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.