Gene detail

Detailed information of OS493_012671-T1 in Lophelia pertusa

Genomic Location: scaffold_33:1883280...1890690
NR annotation: KAJ7379911.1, hypothetical protein OS493_012671 [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
Q9Z2Q4	Methionine synthase OS=Rattus norvegicus OX=10116 GN=Mtr PE=1 SV=1
Q4JIJ3	Methionine synthase OS=Bos taurus OX=9913 GN=MTR PE=2 SV=1
A6H5Y3	Methionine synthase OS=Mus musculus OX=10090 GN=Mtr PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002664 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02574 all species →	S-methyl_trans	Homocysteine S-methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003726 all species →	Domain	Homocysteine-binding domain	Interproscan
IPR050554 all species →	Family	Methionine Synthase/Corrinoid	Interproscan
IPR036589 all species →	Homologous_superfamily	Homocysteine-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45833 all species →	METHIONINE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0008705 all species →	Molecular Function	methionine synthase activity	Interproscan
GO:0009086 all species →	Biological Process	methionine biosynthetic process	Interproscan
GO:0046653 all species →	Biological Process	tetrahydrofolate metabolic process	Interproscan
GO:0050667 all species →	Biological Process	homocysteine metabolic 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K00548	metH, MTR; 5-methyltetrahydrofolate--homocysteine methyltransferase	EC:2.1.1.13	Cobalamin transport and metabolism	ko04980	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_012671-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

108TPM > 0

7Conditions

16.0Max TPM

5.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.52	8.09
polyp at pH7 6	18	18	4.97	7.59
coral polyp · control treatment	16	16	8.34	16.04
coral polyp · oil and dispersant treatment	16	16	5.01	11.48
coral polyp · oil treatment	16	16	5.78	12.04
coral polyp · dispersant treatment	16	15	6.36	13.50
Polyp	10	9	2.39	4.12

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.09
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.39
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.42
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.10
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.08
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.76
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.11
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.09
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.80
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.29
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.57
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.56
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.39
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.03
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.54
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.54
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.34
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.58
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.56
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.56
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.32
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.51
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.67
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.04
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.44
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.97
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.58
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.08
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.43
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.16
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.84
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.68
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.48
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.43
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.88
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.46
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.42
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.74
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.37
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.27
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.30
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.22
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.04
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.17
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.67
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.06
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.93
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.70
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.80
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.37
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.63
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.94
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.10
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.50
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.14
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.24
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.53
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.48
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.49
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.45
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.07
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.84
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.52
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.12
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.08
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.94
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.53
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.20
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.33
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.09
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.