Gene detail

Detailed information of OS493_029278-T1 in Lophelia pertusa

Genomic Location: scaffold_176:690903...696620
NR annotation: KAJ7383311.1, Glycosaminoglycan xylosylkinase [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
O75063	Glycosaminoglycan xylosylkinase OS=Homo sapiens OX=9606 GN=FAM20B PE=1 SV=1
Q8VCS3	Glycosaminoglycan xylosylkinase OS=Mus musculus OX=10090 GN=Fam20b PE=1 SV=1
Q5RH51	Glycosaminoglycan xylosylkinase OS=Danio rerio OX=7955 GN=fam20b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006682 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06702 all species →	Fam20C	Golgi casein kinase, C-terminal, Fam20	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR024869 all species →	Family	FAM20	Interproscan
IPR009581 all species →	Domain	FAM20, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12450 all species →	DENTIN MATRIX PROTEIN 4 PROTEIN FAM20	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005794 all species →	Cellular Component	Golgi apparatus	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	Interproscan
GO:0016773 all species →	Molecular Function	phosphotransferase activity, alcohol group as acceptor	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_029278-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_029278-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

11.7Max TPM

5.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.38	7.69
polyp at pH7 6	18	17	4.40	7.53
coral polyp · control treatment	16	16	8.26	11.10
coral polyp · oil and dispersant treatment	16	16	6.94	11.70
coral polyp · oil treatment	16	16	5.56	7.89
coral polyp · dispersant treatment	16	15	6.45	9.82
Polyp	10	10	3.09	7.38

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.95
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.65
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.17
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.94
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.34
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.16
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.92
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.59
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.53
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.97
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.54
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.53
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.30
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.07
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.96
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.91
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.35
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.29
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.03
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.96
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.93
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.78
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.77
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.64
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.58
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.53
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.10
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.05
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.53
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.51
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.49
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.86
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.24
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.48
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.08
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.07
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.73
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.44
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.92
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.99
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.12
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.32
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.93
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.73
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.56
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.71
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.26
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.15
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.15
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.94
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.78
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.38
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.05
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.82
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.62
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.50
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.71
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.82
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.31
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.33
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.19
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.75
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.69
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.43
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.80
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.17
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.09
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.68
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.40
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.39
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.38
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.05
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.28
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.52
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.42
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.40
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.31
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.95
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.12

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.