Gene detail

Detailed information of XP_068743679.1 in Montipora capricornis

Genomic Location: chr1:37920866...37937746
NR annotation: XP_029190504.2, LOW QUALITY PROTEIN: serine hydroxymethyltransferase, mitochondrial-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068887578.1

CAGGCTCAGTTTGTATTTTCACTTGTAGTAGGAAAATAACCTGTCACTCTGCTATTGAATTGCACACTTcctgtttatttctttatttctttcttcgGTGTTTTATCTTTGAAAGTCCAGAATGTCGTCTTTTACTCGTAAAATTGTACCTCTCCAGTCTTGTTGGAACAGTCTCTTTGGCAATGTAGGTTTTCAGTCTGCATGTTGTTTGTCTATACTTCGGCGCACTATTTGGACAGGCCAAGAGGCACTGGAAGATGATGACCCAGAGATGTACGACTTGATCAAACAGGAGAAAGACAGACAAGTGAGGGGACTGGAACTCATTGCATCTGAGAATTTCTGCAGCCGTGCAGCTTTAGAGGCCATGGGATCCTGTTTGAATAATAAATACTCCGAGGGTTATCCTGGGCAAAGGTATTATGGTGGAACACAAATTATTGATAAAGTTGAACGACTTGTTCAGAAAAGGGCATTGGAAGCTTTCAACTTAGATCCAAAGGAATGGGGTGTTAATGTACAGCCATACTCAGGATCACCCGCCAATTTTGCAGCTTATACAGGTCTTTTAAAACCACATGATCGAATTATGGGACTTGACCTGCCACATGGGGGACAtttaacTCATGGATTTATGACTGATGCAAAGAGGATTTCTGCAACATCTATTTATTTTGAGTCAATGCCTTACCGACTTAACgAAGAAACTGGGCTAATTGACTATGATAAGCTGCAAGAAAATGCTCGTCTTTTCCGTCCTCGATTAATCATAGCCGGAGCAAGTGCATACTCTAGACTTTATGACTACCAGAGAATGAGAGAGataGCAGATGAACATAAAGCTGTTTTGCTGGCCGATATTGCCCATATAAGTGGCCTTATAGCTGCACAGgTCATTCCCAGCCCATTTGATCATGTTCACGTTGTAACAACCACAACGCACAAGACTCTACGGGCTGTTAGAGCAGGATTAATTTTCTATCGTGTTGgagtcaaaggaaaaaacaagaaaactggGAAAGATATCATGTATGACTTTGACAAGAACATTGACTTCGCAGTGTTCCCTTCCCTTCAAGGAGGCCCTCACAACCATGCTATTGCTGGCGTAGGTGTAGCACTCAAACAGGCACAAACACCAATGTTTAAAGAATATCAGCAGCAAGTTCTGAAGAATGCTAAAGCCATGGCAAAAGCTTTATCAGAGTCAGGTTATTCCATGGTGTCAGGTGGGACTGATAACCATCTGGTTTTGCTTGACTTAAGGCCCAAGGGAATTGATGGAGCGCGTGTGGAGAAGGTCCTGGAAATGGCCTCCATCACAGCAAACAAAAATACATGTCCAGGAGACAAGAGTGCACTGAAACCAGGCGGGCTAAGATTAGGTGTGCCTGCGCTTACATCTCGTAATTTTAAGGAAAACGACTTTGTAAAGGTTGTGGAGTTTCTCGACCGGGGAGTGAAGATAGCTTTGGAAGCTCAGCATGCCACGGgTGATGTTATGAAAGACTTCCTATCGTACATAGAGTCCAACGCGGAAACAAAAGCAAAGATTGCTTCACTTAGGATAGAGGTGGAGAGTTTCGCCAGAAGATTTCCAATGCCAGGATTTGACGAGCGCTGAAGGGAACATGGTACAAGTACAACATATTGATTATTGTTTAGGAACAAAGGGGAAAAGACTTTTAATTCTCATTCAATTgtagacaaagacaaaggatgTTCTTTTCTTATGAGGGAATCACCAATTccttttcaggggcacccaacgtcaattttcggaaaatatctgttcggaagacgatttgagatctagaattttcggtacatttgttgtaaaatgtcttgcttgcctgcctgcctctcctaggattatCGAACATCTACAAAATGGTATATAATTACCCCTTTTTAACGAATTTTTAcactaaaaaggtcacctagaatttctgggaaccttttttctggctgaaattttcgaaaaggtcaGTTTTTATTTCTAGAATTTTcgaatcactagactttcagctaggaaatccgaacagatgaaacatttttaggggataaaaatatgcctacatctgccgtttaaataccaaaatacgtgtaacaatgctatgtttaagtggttttgaactatgttctcgttgggtgcccctggcttTTGTCGCGCATGCACGTGCTGGCGGCCACCGGTCATGCTGCAAGTGTTCCGCCACAATCCAAACACACTTCCACCACCAGAAAGGCCTTTGGTAATCATAATTCAAATCTTTGGATTATGAGCCGCGAACACGTGCACTACTTGAAAACGTCAAGTGATCTTTAAACATATCAAATCAATCGATGGTTTTTATTGACTATCATCTTAAAAGTCTCTCGGGAACGAAGTACAATCCTAGGCAAATAAATTTGTTCACGTAAGGAATTTTCGTGCCATTATCCAAAGCAAACTATGTTACACGAGGACTTGTACCATTGATCAACCTTTTCCCCTTCATATTCAATGTTGAATGTCCAAAAGTTCATGTCGTTGAGTGTCATCAGCTTAGTTCGAGTCAACGTTGATTAGATGGAAGGGGAGGGAAAAGGTACGAGGTGGTCAGGAAAGAGAGACATATGCAGGGGTGTCCCACTGTAATTTGTCTAGGATCGTAGTTCGACCGGCATAAGTCGAAGAGTCCAATTCTCGACCCCGTGCCATCATGGTGGAAGACGAGTGATGTCGCTTTCAGCTGTTTTGGGCGGAAGTTAGTCGAAGCCAAAAATAGAATCAATATTGTTAGATAACAATACACGTGTAAATTTACATACATTACAAAAGTGTTCTAATAACACCCAAAGCATTCAGTTTCATGTTCTTTCCATATTTTTGCCTGCACACAGGCTCTCTGTGTGTTTTATTGTTGGGGAATTGGAGCCCCAAACCGATTTACTGCACGGAGAGCCTGTGTGCAGGATATCCATATTTTTGGATCAAAAACGTGAGATGTGAAAAGAGATGAAAGACAGCTACGGTGTATAATTACACACTGGACATCTCTTTGGTGGCTTAGTATTTGGTGAAAGAGAAATGCCTGTCAAAATTCGTGCAGTTGGTTTCTTCACTTTTAACCTATCACACCTAATACATCAGTTATGTAATGTACCGAAATCTCCACAGAATCGTGGGCATGACaagtgaaataaaatattatgcaTTACTTTGCGAAGTAAGGAATTAATTCATTTAATAACCCTTCATATATTTTATAGGCTCAGATTTCTAGCAAAATTCGAGATAGCGAACTAAATGTtaggggaaaaaaaaatcataatttATTCAATACCAGTATTATTAGACCGTCGACATAATATTTTGCAATGTTATCAAAGCTGTACTGAACCTTAGAAGGGGCTCGGATACAACCATAGTTAATGGAAaagactggtttggaagctcggcaaacatcaaaggagcaaacaaagatgccaagatttaggttggaaagtccacgaccgtgcacaatcttttgttttgcgctcatacactattcataaattacgtaaccaacacgtttctattggttagttcctcaatacggagtaaacaaccattgtcttttgtgcacggtcaaggccaaaaaagagaacaaaaacctacaacaaagaaagttgtcaggtttcataaccattctcgtctattaactatgatacAACACAACTCCTTAAGAGCTCTGAAAGTCGCAGAAATGACGATTTTCGAATACGAGGAACTTCGCTCTTGTTTTCTTAGTTGTTGGCAAACACGAATTGCCTTTAAGATTTTTTGTACGATGTCTTTGGCAATTCAGTTTGTAGTGAAAATTTTCCAAGTTCTAGCTATCTCAGGCCAAATGGTTCTTCAGTTTATGAATTTCATGACATAAACTGAATAAAATTTACTTGTCAATCGAACACAATGAAACTCTAAAATGccgcaaaaataaaaataacggGTGTATATTCGTATATTAGTGTTTAATAAAGTGATTatctcaataaaaaaattgtcaaattctTAAATAAATAGTTATATATTGTAGGAGTTGCTGTCCTTTGAACACTTTTAGGTTGAGAAGTCCAAATGACACCAATTTAATGTGGCAATATTCAGGAGCTTGGCTCCCTCAATTTTAATTCGTTTGAAGGTATAGTTTAGGACTTGAAGGCCTAATTTTGTTGGCTGGCATTCAATTCCGTTTTATAAAATTTTCTTTGattaaaagagaaagaaaaatagaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
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
Q3SZ20	Serine hydroxymethyltransferase, mitochondrial OS=Bos taurus OX=9913 GN=SHMT2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001352 (this species only) · gene tree & orthology

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
IPR039429 all species →	Domain	Serine hydroxymethyltransferase-like domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan
IPR001085 all species →	Family	Serine hydroxymethyltransferase	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
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 XP_068743679.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples

29TPM > 0

1Conditions

46.1Max TPM

22.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	29	22.33	46.06

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	46.06
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	46.01
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	41.20
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	39.81
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	38.72
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	37.48
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	36.60
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	35.85
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	34.94
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	34.74
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	34.56
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	32.68
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	26.77
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	26.21
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	26.09
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	26.07
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	26.00
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	25.84
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	21.70
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	20.45
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	19.57
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	18.15
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	18.03
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	17.76
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	17.48
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	16.62
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	14.30
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	12.25
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	11.83
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora capricornis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	14	XP_068750222.1	0.947030940012159
Negatively correlated	3	XP_068724527.1	-0.469928897748482

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora capricornis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →