Gene detail

Detailed information of OS493_007656-T1 in Lophelia pertusa

Genomic Location: scaffold_17:567300...568861
NR annotation: KAJ7365017.1, Calcium and integrin-binding member 2 [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
O75838	Calcium and integrin-binding family member 2 OS=Homo sapiens OX=9606 GN=CIB2 PE=1 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)	OG0002704 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13499 all species →	EF-hand_7	EF-hand domain pair	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051433 all species →	Family	Calcium and Integrin-Binding	Interproscan
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	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_007656-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_007656-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

82TPM > 0

7Conditions

21.2Max TPM

2.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	3.61	13.25
polyp at pH7 6	18	9	1.33	8.03
coral polyp · control treatment	16	14	3.87	8.61
coral polyp · oil and dispersant treatment	16	12	2.15	5.68
coral polyp · oil treatment	16	15	3.03	7.22
coral polyp · dispersant treatment	16	12	1.14	4.45
Polyp	10	7	4.88	21.16

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	-	13.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.16
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.44
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.36
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.12
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.74
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.78
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.47
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.46
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.21
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.92
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
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
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.03
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.19
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.16
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.05
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
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
SRR11359515	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
SRR11359524	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
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.61
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.14
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.33
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.77
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.42
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.78
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.74
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.72
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.62
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.54
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.54
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.46
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
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.68
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.72
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.98
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.71
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.88
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.79
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
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.22
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.76
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.44
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.21
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.82
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.69
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.85
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.03
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.27
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.94
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.90
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.36
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.45
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.87
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.41
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.17
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.05
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.90
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR16705953	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
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	-	21.16
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.70
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.08
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.82
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.38
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.13
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.