Gene detail

Detailed information of OS493_007657-T1 in Lophelia pertusa

Genomic Location: scaffold_17:568885...572468
NR annotation: KAJ7365018.1, Calcium and integrin-binding member 3 [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
Q6PC72	Calcium and integrin-binding family member 2 OS=Danio rerio OX=7955 GN=cib2 PE=2 SV=1
Q9Z309	Calcium and integrin-binding family member 2 OS=Mus musculus OX=10090 GN=Cib2 PE=1 SV=1
Q568Z7	Calcium and integrin-binding family member 2 OS=Rattus norvegicus OX=10116 GN=Cib2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002832 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_007657-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR051433 all species →	Family	Calcium and Integrin-Binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45791 all species →	CALCIUM AND INTEGRIN BINDING FAMILY MEMBER 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000287 all species →	Molecular Function	magnesium ion binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0055074 all species →	Biological Process	calcium ion homeostasis	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_007657-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_007657-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

73TPM > 0

7Conditions

7.3Max TPM

0.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	10	0.54	1.98
polyp at pH7 6	18	6	0.36	2.05
coral polyp · control treatment	16	14	1.59	3.59
coral polyp · oil and dispersant treatment	16	14	0.93	3.54
coral polyp · oil treatment	16	14	1.12	3.33
coral polyp · dispersant treatment	16	9	0.62	2.76
Polyp	10	6	1.89	7.27

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.56
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.24
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.99
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.97
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.90
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.50
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.49
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.28
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.74
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.51
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.12
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
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	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
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.59
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.78
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.76
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.21
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.02
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.48
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.22
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.98
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.82
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.77
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.54
SRR16706004	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	1.79
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.02
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.60
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.57
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.54
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.54
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.17
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.42
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.56
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.49
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.42
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.10
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.92
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.45
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.40
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705967	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
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.27
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.03
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.12
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.80
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.81
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.