Gene detail

Detailed information of OS493_039840-T1 in Lophelia pertusa

Genomic Location: scaffold_1478:6825...8652
NR annotation: KAJ7381656.1, 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
P34897	Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3
Q3SZ20	Serine hydroxymethyltransferase, mitochondrial OS=Bos taurus OX=9913 GN=SHMT2 PE=2 SV=1
P14519	Serine hydroxymethyltransferase, mitochondrial OS=Oryctolagus cuniculus OX=9986 GN=SHMT2 PE=1 SV=2

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
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR039429 all species →	Domain	Serine hydroxymethyltransferase-like domain	Interproscan
IPR049943 all species →	Family	Serine hydroxymethyltransferase-like	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	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: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:0019264 all species →	Biological Process	glycine biosynthetic process from serine	Interproscan
GO:0030170 all species →	Molecular Function	pyridoxal phosphate 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

No KEGG orthology assignment for OS493_039840-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_039840-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

164.8Max TPM

48.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	42.82	74.94
polyp at pH7 6	18	18	46.46	72.68
coral polyp · control treatment	16	16	52.06	95.11
coral polyp · oil and dispersant treatment	16	16	85.61	164.81
coral polyp · oil treatment	16	16	45.38	70.23
coral polyp · dispersant treatment	16	16	29.60	75.87
Polyp	10	10	31.40	44.63

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	-	74.94
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	71.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.85
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.77
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.52
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.15
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.92
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.29
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.62
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.33
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.10
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.71
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.19
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.31
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.12
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.07
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.06
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.97
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.65
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.61
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.71
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.65
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.51
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.43
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.14
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.11
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.42
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.04
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.66
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.87
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.15
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.96
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.01
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.98
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.80
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.43
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.80
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.82
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	164.81
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	142.53
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.63
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	110.65
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.34
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.05
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.07
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.86
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.86
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.48
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.46
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.09
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.48
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.23
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.48
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.02
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.55
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.03
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.14
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.99
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.31
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.43
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.08
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.41
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.87
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.53
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.68
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.40
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.42
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.23
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.21
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.91
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.66
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.92
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.01
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	44.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	36.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	35.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	34.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	33.18
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	30.37
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	29.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.12
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	24.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	18.06

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.