Gene detail

Detailed information of OS493_031715-T1 in Lophelia pertusa

Genomic Location: scaffold_224:295312...302851
NR annotation: KAJ7382939.1, hypothetical protein OS493_031715 [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
P02469	Laminin subunit beta-1 OS=Mus musculus OX=10090 GN=Lamb1 PE=1 SV=3
P15800	Laminin subunit beta-2 OS=Rattus norvegicus OX=10116 GN=Lamb2 PE=1 SV=1
Q61292	Laminin subunit beta-2 OS=Mus musculus OX=10090 GN=Lamb2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003124 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00053 all species →	Laminin_EGF	Laminin EGF domain	Domain	Interproscan
PF00055 all species →	Laminin_N	Laminin N-terminal (Domain VI)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002049 all species →	Domain	Laminin-type EGF domain	Interproscan
IPR008211 all species →	Domain	Laminin, N-terminal	Interproscan
IPR050440 all species →	Family	Laminin/Netrin Extracellular Matrix	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10574 all species →	NETRIN/LAMININ-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0009887 all species →	Biological Process	animal organ morphogenesis	Interproscan
GO:0009888 all species →	Biological Process	tissue development	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0034446 all species →	Biological Process	substrate adhesion-dependent cell spreading	Interproscan
GO:0043256 all species →	Cellular Component	laminin complex	Interproscan
GO:0070831 all species →	Biological Process	basement membrane assembly	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_031715-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_031715-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

99TPM > 0

7Conditions

15.8Max TPM

3.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	1.75	3.15
polyp at pH7 6	18	14	2.53	5.31
coral polyp · control treatment	16	16	4.62	9.82
coral polyp · oil and dispersant treatment	16	15	3.20	8.54
coral polyp · oil treatment	16	15	3.76	15.77
coral polyp · dispersant treatment	16	15	4.23	10.93
Polyp	10	7	0.47	1.12

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.15
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.62
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.57
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.56
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.29
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.12
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.69
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.43
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.21
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.90
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.31
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.22
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.77
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.75
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.71
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.71
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.71
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.65
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.38
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.72
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.26
SRR11359501	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
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
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.82
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.68
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.16
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.80
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.67
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.59
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.40
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.23
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.33
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.98
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.78
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.73
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.54
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.94
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.96
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.95
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.90
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.54
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.52
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.65
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.36
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.09
SRR16705977	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	15.77
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.85
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.96
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.88
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.97
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.96
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.93
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.16
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.06
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.79
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.93
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.71
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.20
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.57
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.42
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.30
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.47
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.83
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.47
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.05
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.90
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.83
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.93
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.53
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.12
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.09
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.70
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.33
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.26
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.06
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025712	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.