Gene detail

Detailed information of OS493_009973-T1 in Lophelia pertusa

Genomic Location: scaffold_24:1291700...1302436
NR annotation: KAJ7337121.1, hypothetical protein OS493_009973 [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
P22676	Calretinin OS=Homo sapiens OX=9606 GN=CALB2 PE=1 SV=2
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

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
PF13202 all species →	EF-hand_5	EF hand	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051001 all species →	Family	Calbindin Calcium-Binding	Interproscan
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	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

No KEGG orthology assignment for OS493_009973-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_009973-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

329.7Max TPM

57.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	43.97	78.59
polyp at pH7 6	18	18	39.23	65.86
coral polyp · control treatment	16	16	72.05	158.05
coral polyp · oil and dispersant treatment	16	16	56.55	139.45
coral polyp · oil treatment	16	16	50.70	145.23
coral polyp · dispersant treatment	16	16	60.40	123.49
Polyp	10	10	99.93	329.69

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	-	78.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.80
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.30
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.95
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.20
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.85
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.54
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.17
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.83
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.03
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.34
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.95
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.86
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.30
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.18
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.84
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.86
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.54
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.20
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.15
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.59
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.97
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.97
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.89
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.43
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.37
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.14
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	158.05
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	152.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	122.31
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.84
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.70
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.04
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.19
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.34
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.47
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.67
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.54
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.02
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.91
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.44
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.31
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.45
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.18
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.72
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.40
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.86
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.22
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.71
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.37
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.74
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.01
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.07
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.41
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.86
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	145.23
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.94
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.81
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.86
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.22
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.42
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.12
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.72
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.49
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.19
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.68
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	123.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	107.56
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.77
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.87
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.39
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.15
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.32
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.85
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.32
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.36
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	329.69
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	207.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	124.52
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	121.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	68.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	47.90
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	42.74
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	29.70
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.03
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	12.55

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.