Gene detail

Detailed information of OS493_017421-T1 in Lophelia pertusa

Genomic Location: scaffold_55:2270392...2271790
NR annotation: KAJ7391723.1, hypothetical protein OS493_017421 [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
A1L1V4	Lysyl oxidase homolog 2B OS=Danio rerio OX=7955 GN=loxl2b PE=2 SV=1
B8A4W9	Lysyl oxidase homolog 3B OS=Danio rerio OX=7955 GN=loxl3b PE=2 SV=1
F1QQC3	Lysyl oxidase homolog 2A OS=Danio rerio OX=7955 GN=loxl2a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001610 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00040 all species →	fn2	Fibronectin type II domain	Domain	Interproscan
PF01186 all species →	Lysyl_oxidase	Lysyl oxidase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000562 all species →	Domain	Fibronectin type II domain	Interproscan
IPR050912 all species →	Family	Lysyl oxidase-like protein	Interproscan
IPR013806 all species →	Homologous_superfamily	Kringle-like fold	Interproscan
IPR036943 all species →	Homologous_superfamily	Fibronectin type II domain superfamily	Interproscan
IPR001695 all species →	Family	Lysyl oxidase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45817 all species →	LYSYL OXIDASE-LIKE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004720 all species →	Molecular Function	protein-lysine 6-oxidase activity	Interproscan
GO:0005615 all species →	Cellular Component	extracellular space	Interproscan
GO:0018057 all species →	Biological Process	peptidyl-lysine oxidation	Interproscan
GO:0005507 all species →	Molecular Function	copper ion binding	Interproscan
GO:0016641 all species →	Molecular Function	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen 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_017421-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_017421-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

102TPM > 0

7Conditions

16.1Max TPM

3.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	3.11	5.62
polyp at pH7 6	18	15	3.14	7.50
coral polyp · control treatment	16	16	3.50	6.11
coral polyp · oil and dispersant treatment	16	15	4.07	16.13
coral polyp · oil treatment	16	16	3.37	8.71
coral polyp · dispersant treatment	16	14	2.85	9.63
Polyp	10	9	1.10	1.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.62
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.09
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.07
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.91
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.15
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.14
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.74
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.23
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.01
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.89
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.68
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.08
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.66
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.07
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.89
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.35
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.24
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.20
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.58
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.32
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.08
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.06
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
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.11
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.38
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.85
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.64
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.36
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.15
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.09
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.89
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.71
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.42
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.13
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.47
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.70
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.45
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.91
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.04
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.59
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.53
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.99
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.55
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.30
SRR16705994	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	8.71
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.49
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.73
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.91
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.61
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.54
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.36
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.87
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.16
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.87
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.69
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.63
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.48
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.25
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.99
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.37
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.51
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.36
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.08
SRR16705953	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
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.96
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.93
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.75
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.49
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.10
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.78
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.71
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.38
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.