Gene detail

Detailed information of OS493_014741-T1 in Lophelia pertusa

Genomic Location: scaffold_42:1073674...1076740
NR annotation: KAJ7334427.1, hypothetical protein OS493_014741 [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
Q9VE46	High-affinity choline transporter 1 OS=Drosophila melanogaster OX=7227 GN=ChT PE=2 SV=2
O02228	High-affinity choline transporter 1 OS=Caenorhabditis elegans OX=6239 GN=cho-1 PE=2 SV=2
Q9GZV3	High affinity choline transporter 1 OS=Homo sapiens OX=9606 GN=SLC5A7 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001039 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00474 all species →	SSF	Sodium:solute symporter family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052244 all species →	Family	High-affinity choline transporter	Interproscan
IPR001734 all species →	Family	Sodium/solute symporter	Interproscan
IPR038377 all species →	Homologous_superfamily	Sodium/glucose symporter superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45897 all species →	HIGH-AFFINITY CHOLINE TRANSPORTER 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005307 all species →	Molecular Function	choline:sodium symporter activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008292 all species →	Biological Process	acetylcholine biosynthetic process	Interproscan
GO:0015871 all species →	Biological Process	choline transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14387	SLC5A7, CHT1; solute carrier family 5 (high affinity choline transporter), member 7	-	Transporters	ko02000	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_014741-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

108.3Max TPM

27.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.93	38.70
polyp at pH7 6	18	18	32.92	81.76
coral polyp · control treatment	16	16	29.36	52.37
coral polyp · oil and dispersant treatment	16	16	28.67	73.04
coral polyp · oil treatment	16	16	36.83	108.26
coral polyp · dispersant treatment	16	16	29.93	82.34
Polyp	10	10	6.49	13.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.26
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.65
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.07
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.80
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.10
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.20
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.79
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.30
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.27
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.55
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.43
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.57
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.95
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.61
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.50
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.76
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.02
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.55
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.49
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.68
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.77
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.78
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.99
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.13
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.56
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.37
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.17
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.85
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.63
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.92
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.30
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.70
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.02
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.40
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.89
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.09
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.48
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.67
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.09
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.38
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.73
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.71
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.51
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.95
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.67
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.85
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.98
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.91
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.89
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	108.26
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.39
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.34
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.62
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.70
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.39
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.02
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.78
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.13
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.09
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.15
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.17
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.05
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.97
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.58
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.97
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.82
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.10
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.77
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.94
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.03
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.38
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.62
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.98
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.23
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.46
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.14
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.69
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.99
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.35
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.66
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.49
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.06

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.