Gene detail

Detailed information of OS493_017425-T1 in Lophelia pertusa

Genomic Location: scaffold_55:2322655...2325354
NR annotation: KAJ7391727.1, lysyl oxidase-like 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
F1RD85	Lysyl oxidase homolog 3A OS=Danio rerio OX=7955 GN=loxl3a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000074 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00530 all species →	SRCR	Scavenger receptor cysteine-rich domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001190 all species →	Domain	SRCR domain	Interproscan
IPR017448 all species →	Domain	SRCR-like domain	Interproscan
IPR036772 all species →	Homologous_superfamily	SRCR-like domain superfamily	Interproscan
IPR050912 all species →	Family	Lysyl oxidase-like protein	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
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

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_017425-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_017425-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

44.0Max TPM

16.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.76	23.21
polyp at pH7 6	18	18	16.67	28.37
coral polyp · control treatment	16	16	20.77	44.00
coral polyp · oil and dispersant treatment	16	16	17.77	37.18
coral polyp · oil treatment	16	16	20.84	43.03
coral polyp · dispersant treatment	16	16	14.88	30.98
Polyp	10	8	3.30	7.74

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.21
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.05
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.89
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.23
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.14
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.55
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.40
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.24
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.18
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.31
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.37
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.06
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.97
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.20
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.85
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.63
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.20
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.44
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.90
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.04
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.32
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.86
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.99
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.84
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.83
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.52
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.18
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.25
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.65
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.21
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.71
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.12
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.99
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.32
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.97
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.58
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.13
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.18
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.99
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.16
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.26
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.98
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.40
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.85
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.60
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.23
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.09
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.03
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.41
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.39
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.52
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.88
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.16
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.60
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.55
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.94
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.57
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.98
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.72
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.83
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.61
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.93
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.97
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.47
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.66
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.78
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.37
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.23
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.02
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.67
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.94
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.74
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.74
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.84
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.31
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.54
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.17
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.78
SRR7746667	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.