Gene detail

Detailed information of OS493_005284-T1 in Lophelia pertusa

Genomic Location: scaffold_10:4791348...4799670
NR annotation: KAJ7374926.1, Calretinin [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
Q3ZBY3	Calretinin OS=Bos taurus OX=9913 GN=CALB2 PE=2 SV=1
P07090	Calretinin OS=Gallus gallus OX=9031 GN=CALB2 PE=2 SV=3
P22676	Calretinin OS=Homo sapiens OX=9606 GN=CALB2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001296 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13202 all species →	EF-hand_5	EF hand	Domain	Interproscan
PF13499 all species →	EF-hand_7	EF-hand domain pair	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
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
IPR051001 all species →	Family	Calbindin Calcium-Binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19972 all species →	CALBINDIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0043005 all species →	Cellular Component	neuron projection	Interproscan
GO:0045202 all species →	Cellular Component	synapse	Interproscan
GO:0051480 all species →	Biological Process	regulation of cytosolic calcium ion concentration	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K23908	CALB2; calretinin	-	Domain-containing proteins not elsewhere classified	ko04990	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_005284-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

198.5Max TPM

91.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	66.64	117.63
polyp at pH7 6	18	18	87.38	113.23
coral polyp · control treatment	16	16	118.58	181.21
coral polyp · oil and dispersant treatment	16	16	111.81	157.49
coral polyp · oil treatment	16	16	118.63	198.46
coral polyp · dispersant treatment	16	16	72.02	124.48
Polyp	10	10	57.57	106.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	117.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	109.34
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.53
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	76.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.07
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.42
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.34
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.24
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.15
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.61
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.21
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.67
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.24
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.13
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.46
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.27
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	104.23
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	103.99
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	100.31
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.83
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.31
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.68
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	87.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	86.06
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	79.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.35
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.39
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.06
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.76
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	181.21
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	146.18
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	145.30
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.61
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	131.90
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.68
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	122.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	120.50
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	119.93
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	119.01
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.39
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.75
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.59
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.78
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	157.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	144.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	132.43
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	131.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	127.19
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	126.33
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	125.78
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.67
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.36
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.62
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.55
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.33
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.87
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.64
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	198.46
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	158.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	154.17
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	138.39
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	133.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.19
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	127.14
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	123.29
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	119.39
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	117.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	98.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	95.25
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.12
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.07
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.83
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	124.48
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	108.64
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.62
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.23
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.19
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.08
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.29
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.51
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.96
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.17
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.42
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.13
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.62
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	106.33
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	93.50
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	69.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	67.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	62.43
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	46.86
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	46.38
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	32.54
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	26.03
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	24.53

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.