Gene detail

Detailed information of g1858.t1 in Montipora capitata

Genomic Location: Sc0000025:592658...599825
NR annotation: XP_029191754.2, serine hydroxymethyltransferase, mitochondrial-like isoform X2 [Acropora millepora]
Species Montipora capitata · 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
P34896	Serine hydroxymethyltransferase, cytosolic OS=Homo sapiens OX=9606 GN=SHMT1 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
IPR039429 all species →	Domain	Serine hydroxymethyltransferase-like domain	Interproscan
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan
IPR049943 all species →	Family	Serine hydroxymethyltransferase-like	Interproscan
IPR019798 all species →	Binding_site	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	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 g1858.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

48TPM > 0

3Conditions

116.7Max TPM

46.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	51.77	116.67
whole organisms · low pH treatment	15	15	42.60	92.68
whole organisms · extra low pH treatment pH treatment	12	12	42.04	90.16

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	116.67
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	114.62
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	98.53
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	95.88
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	93.73
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	89.83
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	89.76
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	85.05
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	72.91
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	68.32
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	44.07
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	32.54
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	30.32
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	9.21
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	8.30
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	8.25
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	7.87
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	6.28
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	6.09
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	5.10
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	3.83
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	92.68
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	88.24
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	80.24
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	78.58
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	75.88
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	70.20
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	42.53
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	37.17
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	31.25
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	12.11
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	8.84
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.48
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	5.33
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	4.69
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	3.83
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	90.16
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	89.10
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	85.66
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	73.06
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	68.70
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	29.35
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	29.00
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	14.28
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	10.40
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	6.43
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	5.01
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.35

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.