Gene detail

Detailed information of OS493_028820-T1 in Lophelia pertusa

Genomic Location: scaffold_169:545236...553570
NR annotation: KAJ7389851.1, Serine hydroxymethyltransferase 2 [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
Q3SZ20	Serine hydroxymethyltransferase, mitochondrial OS=Bos taurus OX=9913 GN=SHMT2 PE=2 SV=1
P34897	Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3
Q9CZN7	Serine hydroxymethyltransferase, mitochondrial OS=Mus musculus OX=10090 GN=Shmt2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001347 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00464 all species →	SHMT	Serine hydroxymethyltransferase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001085 all species →	Family	Serine hydroxymethyltransferase	Interproscan
IPR049943 all species →	Family	Serine hydroxymethyltransferase-like	Interproscan
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR039429 all species →	Domain	Serine hydroxymethyltransferase-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11680 all species →	SERINE HYDROXYMETHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004372 all species →	Molecular Function	glycine hydroxymethyltransferase activity	Interproscan
GO:0019264 all species →	Biological Process	glycine biosynthetic process from serine	Interproscan
GO:0030170 all species →	Molecular Function	pyridoxal phosphate binding	Interproscan
GO:0035999 all species →	Biological Process	tetrahydrofolate interconversion	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006565 all species →	Biological Process	L-serine catabolic process	Interproscan
GO:0006730 all species →	Biological Process	one-carbon metabolic process	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0046653 all species →	Biological Process	tetrahydrofolate metabolic process	Interproscan
GO:0046655 all species →	Biological Process	folic acid metabolic process	Interproscan
GO:0050897 all species →	Molecular Function	cobalt ion binding	Interproscan
GO:0070905 all species →	Molecular Function	serine binding	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
K00600	glyA, SHMT; glycine hydroxymethyltransferase	EC:2.1.2.1	Antifolate resistance	ko01523	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_028820-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

134.1Max TPM

44.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	34.30	54.70
polyp at pH7 6	18	18	37.79	49.06
coral polyp · control treatment	16	16	50.69	102.83
coral polyp · oil and dispersant treatment	16	16	77.18	134.06
coral polyp · oil treatment	16	16	46.21	84.75
coral polyp · dispersant treatment	16	16	34.73	63.76
Polyp	10	10	27.55	40.04

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	-	54.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.30
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.67
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.36
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.24
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.00
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.03
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.65
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.67
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.19
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.74
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.29
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.21
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.93
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.06
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.04
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.80
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.65
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.50
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.26
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.56
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.37
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.39
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.60
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.46
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.42
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.20
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.81
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.49
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	102.83
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.58
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.13
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.46
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.44
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.21
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.41
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.45
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.42
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.58
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.17
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.06
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.81
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.48
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.48
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.70
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	80.66
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.43
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.33
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.49
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.39
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.37
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.75
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.97
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.69
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.29
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.77
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.93
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.72
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.97
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.71
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.33
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.31
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.33
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.76
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.05
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.67
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.98
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.34
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.49
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.73
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.81
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.63
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.76
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.57
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.85
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	40.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	34.45
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	33.49
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	30.62
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	30.52
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	27.83
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.05
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	19.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	18.57
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.32

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.