Gene detail

Detailed information of OS493_003143-T1 in Lophelia pertusa

Genomic Location: scaffold_6:5704744...5712662
NR annotation: KAJ7340399.1, Voltage-dependent T-type calcium channel subunit alpha-1G [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
O43497	Voltage-dependent T-type calcium channel subunit alpha-1G OS=Homo sapiens OX=9606 GN=CACNA1G PE=1 SV=3
O54898	Voltage-dependent T-type calcium channel subunit alpha-1G OS=Rattus norvegicus OX=10116 GN=Cacna1g PE=1 SV=2
Q9Z0Y8	Voltage-dependent T-type calcium channel subunit alpha-1I OS=Rattus norvegicus OX=10116 GN=Cacna1i PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001282 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00520 all species →	Ion_trans	Ion transport protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027359 all species →	Homologous_superfamily	Voltage-dependent channel domain superfamily	Interproscan
IPR043203 all species →	Family	Voltage-gated cation channel calcium and sodium	Interproscan
IPR005821 all species →	Domain	Ion transport domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10037 all species →	VOLTAGE-GATED CATION CHANNEL CALCIUM AND SODIUM	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0001518 all species →	Cellular Component	voltage-gated sodium channel complex	Interproscan
GO:0005248 all species →	Molecular Function	voltage-gated sodium channel activity	Interproscan
GO:0005261 all species →	Molecular Function	monoatomic cation channel activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008332 all species →	Molecular Function	low voltage-gated calcium channel activity	Interproscan
GO:0043005 all species →	Cellular Component	neuron projection	Interproscan
GO:0070509 all species →	Biological Process	calcium ion import	Interproscan
GO:0086010 all species →	Biological Process	membrane depolarization during action potential	Interproscan
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	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_003143-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_003143-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

80TPM > 0

7Conditions

2.5Max TPM

0.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	0.50	1.40
polyp at pH7 6	18	11	0.64	1.82
coral polyp · control treatment	16	15	0.58	1.50
coral polyp · oil and dispersant treatment	16	13	0.38	1.40
coral polyp · oil treatment	16	13	0.65	2.06
coral polyp · dispersant treatment	16	10	0.26	1.28
Polyp	10	7	0.99	2.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.17
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.95
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.78
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.65
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.65
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.55
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.54
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.48
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
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.82
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.47
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.32
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.20
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.83
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.80
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.79
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.25
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.15
SRR11359501	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
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
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.50
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.48
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.29
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.60
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.57
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.52
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.41
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.34
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.28
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.25
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.18
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.17
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.11
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.40
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.12
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.61
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.40
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.40
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.27
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.20
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.12
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.11
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705948	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
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.06
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.26
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.55
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.46
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.45
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.21
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.28
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.66
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.52
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.34
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.26
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.26
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.07
SRR16705953	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
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705969	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
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.46
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.24
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.62
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.54
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.11
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.29
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.