Gene detail

Detailed information of CAB3981542.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3981542.1, serine hydroxymethyltransferase, mitochondrial-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3981542.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3SZ20	Serine hydroxymethyltransferase, mitochondrial OS=Bos taurus OX=9913 GN=SHMT2 PE=2 SV=1
Q9CZN7	Serine hydroxymethyltransferase, mitochondrial OS=Mus musculus OX=10090 GN=Shmt2 PE=1 SV=1
P34897	Serine hydroxymethyltransferase, mitochondrial OS=Homo sapiens OX=9606 GN=SHMT2 PE=1 SV=3

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
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan
IPR019798 all species →	Binding_site	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Interproscan
IPR039429 all species →	Domain	Serine hydroxymethyltransferase-like domain	Interproscan
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan
IPR049943 all species →	Family	Serine hydroxymethyltransferase-like	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 CAB3981542.1 across 21 RNA-seq samples of Paramuricea clavata. 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.

21Samples

20TPM > 0

4Conditions

107.0Max TPM

46.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	63.18	91.83
apical branchlet · Temperature treatment at T0	6	5	36.65	106.96
apical branchlet · Temperature treatment at T25	5	5	46.87	83.13
apical branchlet · Control at T0	4	4	35.39	45.69

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	91.83
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	82.34
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	75.24
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	58.47
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	47.47
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	23.72
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	106.96
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	47.27
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	25.41
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	20.81
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	19.46
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	83.13
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	79.70
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	41.84
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	22.50
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.16
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	45.69
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	37.71
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	31.85
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	26.30

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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.