Gene detail

Detailed information of OS493_023527-T1 in Lophelia pertusa

Genomic Location: scaffold_104:1196192...1213069
NR annotation: KAJ7384198.1, Integrin beta-1 [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
P11584	Integrin beta-PS OS=Drosophila melanogaster OX=7227 GN=mys PE=1 SV=3
P12607	Integrin beta-1-B OS=Xenopus laevis OX=8355 GN=itgb1-b PE=2 SV=1
P12606	Integrin beta-1-A OS=Xenopus laevis OX=8355 GN=itgb1-a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000809 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07965 all species →	Integrin_B_tail	Integrin beta tail domain	Domain	Interproscan
PF18372 all species →	I-EGF_1	Integrin beta epidermal growth factor like domain 1	Domain	Interproscan
PF00362 all species →	Integrin_beta	Integrin beta chain VWA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012896 all species →	Domain	Integrin beta subunit, tail	Interproscan
IPR015812 all species →	Family	Integrin beta subunit	Interproscan
IPR036349 all species →	Homologous_superfamily	Integrin beta tail domain superfamily	Interproscan
IPR002369 all species →	Domain	Integrin beta subunit, VWA domain	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR040622 all species →	Domain	Integrin beta, epidermal growth factor-like domain 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10082 all species →	INTEGRIN BETA SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005178 all species →	Molecular Function	integrin binding	Interproscan
GO:0005925 all species →	Cellular Component	focal adhesion	Interproscan
GO:0007160 all species →	Biological Process	cell-matrix adhesion	Interproscan
GO:0007229 all species →	Biological Process	integrin-mediated signaling pathway	Interproscan
GO:0008305 all species →	Cellular Component	integrin complex	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0033627 all species →	Biological Process	cell adhesion mediated by integrin	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_023527-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_023527-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

41.3Max TPM

17.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.40	24.59
polyp at pH7 6	18	18	14.82	21.64
coral polyp · control treatment	16	16	25.99	39.61
coral polyp · oil and dispersant treatment	16	16	24.59	40.83
coral polyp · oil treatment	16	16	16.41	41.33
coral polyp · dispersant treatment	16	16	19.64	33.22
Polyp	10	10	7.78	14.55

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.59
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.37
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.64
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.28
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.90
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.96
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.37
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.46
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.96
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.73
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.45
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.50
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.06
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.93
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.59
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.64
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.77
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.21
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.31
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.86
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.52
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.71
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.08
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.64
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.82
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.88
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.61
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.67
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.28
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.17
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.98
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.56
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.57
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.90
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.96
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.17
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.54
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.33
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.44
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.83
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.61
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.20
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.73
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.31
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.31
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.77
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.81
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.22
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.16
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.14
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.79
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.61
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.13
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.10
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.14
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.85
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.34
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.08
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.77
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.54
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.55
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.46
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.13
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.89
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.35
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.51
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.01
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.03
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.44
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.05
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.58
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.80
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.55
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.74
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.94
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.66
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.05
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.36
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.20
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.11
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.13

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.