Gene detail

Detailed information of OS493_022292-T1 in Lophelia pertusa

Genomic Location: scaffold_90:1356237...1365657
NR annotation: KAJ7330677.1, Glypican-4 [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
P51655	Glypican-4 OS=Mus musculus OX=10090 GN=Gpc4 PE=1 SV=2
O75487	Glypican-4 OS=Homo sapiens OX=9606 GN=GPC4 PE=1 SV=4
Q9Y625	Glypican-6 OS=Homo sapiens OX=9606 GN=GPC6 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005994 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01153 all species →	Glypican	Glypican	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001863 all species →	Family	Glypican	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10822 all species →	GLYPICAN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005576 all species →	Cellular Component	extracellular region	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0009966 all species →	Biological Process	regulation of signal transduction	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0045202 all species →	Cellular Component	synapse	Interproscan
GO:0062023 all species →	Cellular Component	collagen-containing extracellular matrix	Interproscan
GO:1905475 all species →	Biological Process	regulation of protein localization to 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_022292-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_022292-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

107.2Max TPM

34.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.44	53.81
polyp at pH7 6	18	18	32.95	48.98
coral polyp · control treatment	16	16	35.83	78.30
coral polyp · oil and dispersant treatment	16	16	43.58	106.21
coral polyp · oil treatment	16	16	36.62	107.25
coral polyp · dispersant treatment	16	16	44.47	96.94
Polyp	10	10	13.81	26.12

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	-	53.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.25
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.99
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.54
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.20
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.96
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.38
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.08
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.44
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.60
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.16
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.51
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.42
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.98
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.06
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.69
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.75
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.38
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.40
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.05
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.39
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.83
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.24
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.21
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.94
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.63
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.30
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.43
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.91
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.56
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.75
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.41
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.79
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.14
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.38
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.21
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.11
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.31
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.54
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.05
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.88
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.10
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.57
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.53
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.62
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.33
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.31
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	107.25
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.53
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.73
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.57
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.28
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.26
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.60
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.63
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.36
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.06
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.21
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	88.78
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.15
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.24
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.94
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.22
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.06
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.76
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.21
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	26.12
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.43
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.42
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	15.30
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.05
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.25
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	10.11
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.55
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.08
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.78

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.