Gene detail

Detailed information of OS493_031526-T1 in Lophelia pertusa

Genomic Location: scaffold_219:444034...447586
NR annotation: KAJ7376930.1, hypothetical protein OS493_031526 [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
Q4JAI4	Methionine synthase OS=Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) OX=330779 GN=metE PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002759 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01717 all species →	Meth_synt_2	Cobalamin-independent synthase, Catalytic domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038071 all species →	Homologous_superfamily	UROD/MetE-like superfamily	Interproscan
IPR002629 all species →	Domain	Cobalamin-independent methionine synthase MetE, C-terminal/archaeal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30519 all species →	5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003871 all species →	Molecular Function	5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0009086 all species →	Biological Process	methionine biosynthetic process	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_031526-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_031526-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

106TPM > 0

7Conditions

8.4Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.81	4.37
polyp at pH7 6	18	17	2.95	4.93
coral polyp · control treatment	16	16	1.85	5.63
coral polyp · oil and dispersant treatment	16	15	1.38	4.61
coral polyp · oil treatment	16	15	2.05	3.92
coral polyp · dispersant treatment	16	16	1.61	3.89
Polyp	10	9	2.45	8.39

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.37
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.35
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.49
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.06
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.98
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.61
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.58
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.54
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.93
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.71
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.53
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.93
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.85
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.43
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.57
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.47
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.37
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.09
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.80
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.61
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.59
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.35
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.63
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.33
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.89
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.26
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.20
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.17
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.56
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.49
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.25
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.61
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.56
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.33
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.27
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.25
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.07
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.56
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.92
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.72
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.26
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.16
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.94
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.12
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.78
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.37
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.31
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.10
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.89
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.88
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.68
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.60
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.88
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.67
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.59
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.45
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.31
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.39
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.93
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.01
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.08
SRR7746667	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.