Gene detail

Detailed information of OS493_014745-T1 in Lophelia pertusa

Genomic Location: scaffold_42:1089941...1091788
NR annotation: KAJ7334431.1, hypothetical protein OS493_014745 [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
Q8UWF0	High-affinity choline transporter 1 OS=Torpedo marmorata OX=7788 GN=CHT1 PE=2 SV=1
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
IPR038377 all species →	Homologous_superfamily	Sodium/glucose symporter superfamily	Interproscan
IPR001734 all species →	Family	Sodium/solute symporter	Interproscan
IPR052244 all species →	Family	High-affinity choline transporter	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
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
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

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_014745-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_014745-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

100TPM > 0

7Conditions

13.1Max TPM

3.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	3.25	6.97
polyp at pH7 6	18	14	2.68	5.93
coral polyp · control treatment	16	16	3.48	13.14
coral polyp · oil and dispersant treatment	16	14	2.77	7.35
coral polyp · oil treatment	16	16	4.42	12.85
coral polyp · dispersant treatment	16	15	4.86	11.59
Polyp	10	8	1.50	5.30

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.97
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.20
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.11
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.54
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.53
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.19
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.99
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.94
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.68
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.48
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.08
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.88
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.07
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.93
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.27
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.25
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.01
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.60
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.11
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.87
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.86
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.89
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.76
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.54
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.04
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
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.14
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.54
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.53
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.14
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.08
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.20
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.75
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.97
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.32
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.35
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.59
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.31
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.50
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.10
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.56
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.36
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	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	12.85
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.87
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.61
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.56
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.24
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.99
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.08
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.73
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.54
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.78
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.01
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.55
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.37
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.72
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.59
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.26
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.64
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.53
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.19
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.52
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.30
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.47
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.01
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.87
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.75
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.19
SRR7746667	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.