Gene detail

Detailed information of OS493_005283-T1 in Lophelia pertusa

Genomic Location: scaffold_10:4776321...4789475
NR annotation: KAJ7374925.1, hypothetical protein OS493_005283 [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
Q08331	Calretinin OS=Mus musculus OX=10090 GN=Calb2 PE=1 SV=3
P47728	Calretinin OS=Rattus norvegicus OX=10116 GN=Calb2 PE=1 SV=1
Q3ZBY3	Calretinin OS=Bos taurus OX=9913 GN=CALB2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001318 (this species only)

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
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR051001 all species →	Family	Calbindin Calcium-Binding	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
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_005283-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

522.8Max TPM

123.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	134.17	199.81
polyp at pH7 6	18	18	142.09	215.86
coral polyp · control treatment	16	16	101.91	138.74
coral polyp · oil and dispersant treatment	16	16	96.11	146.29
coral polyp · oil treatment	16	16	107.45	134.91
coral polyp · dispersant treatment	16	16	87.84	157.42
Polyp	10	10	230.79	522.83

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	-	199.81
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	195.47
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	150.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	141.90
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	140.92
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	137.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	136.55
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	134.24
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	132.02
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	122.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	122.06
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	118.87
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	117.84
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	117.44
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	114.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	112.19
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	110.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	110.24
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	215.86
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	192.28
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	180.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	176.37
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	176.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	169.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	168.31
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	166.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	151.01
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	150.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	150.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	140.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.62
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	101.05
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	85.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	84.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.07
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	138.74
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	136.76
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.69
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	125.13
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.89
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.65
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	107.11
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.57
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.93
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.26
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.36
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	146.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	136.31
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	125.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	121.59
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	113.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.57
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	105.27
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.76
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.24
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.75
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.78
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.88
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.77
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	134.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	133.66
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	127.60
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.48
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.24
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	117.80
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	113.95
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	111.64
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	105.34
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.67
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.11
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.81
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.21
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.93
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	157.42
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	145.18
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	125.36
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	97.07
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.28
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.11
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.74
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.10
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.65
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.76
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.77
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.25
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	522.83
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	361.82
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	299.48
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	254.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	239.02
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	200.55
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	132.20
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	130.16
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	93.97
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	73.81

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.