Gene detail

Detailed information of OS493_011155-T1 in Lophelia pertusa

Genomic Location: scaffold_28:974210...978225
NR annotation: KAJ7373553.1, hypothetical protein OS493_011155 [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
Q87NG3	Glycine betaine transporter 1 OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) OX=223926 GN=VP1905 PE=1 SV=1
G3XCN6	Glycine betaine/proline betaine transporter BetS OS=Rhizobium meliloti OX=382 GN=betS PE=1 SV=1
Q24SP9	Probable glycine betaine transporter OS=Desulfitobacterium hafniense (strain Y51) OX=138119 GN=DSY3154 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000591 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02028 all species →	BCCT	BCCT, betaine/carnitine/choline family transporter	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000060 all species →	Family	BCCT transporter family	Interproscan
IPR018093 all species →	Conserved_site	BCCT transporter, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30047 all species →	HIGH-AFFINITY CHOLINE TRANSPORT PROTEIN-RELATED	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:0071705 all species →	Biological Process	nitrogen compound transport	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006810 all species →	Biological Process	transport	Interproscan
GO:0016021 all species →	Cellular Component	membrane	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_011155-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_011155-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

59TPM > 0

7Conditions

0.9Max TPM

0.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	6	0.08	0.30
polyp at pH7 6	18	6	0.09	0.42
coral polyp · control treatment	16	12	0.15	0.61
coral polyp · oil and dispersant treatment	16	9	0.14	0.65
coral polyp · oil treatment	16	12	0.26	0.93
coral polyp · dispersant treatment	16	9	0.15	0.69
Polyp	10	5	0.10	0.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.30
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.27
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.19
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.12
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
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	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
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.42
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.36
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.30
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.25
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.23
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.10
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	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
SRR11359526	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
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.61
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.38
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.37
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.12
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.09
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.08
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.07
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.05
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.04
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.65
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.28
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.21
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.13
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.05
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705947	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
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705982	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
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.93
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.32
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.21
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.15
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.06
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.06
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.69
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.19
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.18
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.10
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.07
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705967	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
SRR16705986	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	-	0.46
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.36
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.12
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.05
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.02
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.00
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.