Detailed information of g29330.t1 in Acropora digitifera

Genomic Location: chr14Alt:2904903...2914725
NR annotation: XP_029203080.1, glycine N-methyltransferase-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P13255Glycine N-methyltransferase OS=Rattus norvegicus OX=10116 GN=Gnmt PE=1 SV=2
Q29555Glycine N-methyltransferase OS=Sus scrofa OX=9823 GN=GNMT PE=1 SV=2
Q14749Glycine N-methyltransferase OS=Homo sapiens OX=9606 GN=GNMT PE=1 SV=3
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF08242
all species →		Methyltransf_12Methyltransferase domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR029063
all species →		Homologous_superfamilyS-adenosyl-L-methionine-dependent methyltransferase superfamilyInterproscan
IPR013217
all species →		DomainMethyltransferase type 12Interproscan
IPR014369
all species →		FamilyGlycine/Sarcosine N-methyltransferaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR16458
all species →		GLYCINE N-METHYLTRANSFERASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0017174
all species →		Molecular Functionglycine N-methyltransferase activityInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0006111
all species →		Biological Processregulation of gluconeogenesisInterproscan
GO:0006730
all species →		Biological Processone-carbon metabolic processInterproscan
GO:0016594
all species →		Molecular Functionglycine bindingInterproscan
GO:0042802
all species →		Molecular Functionidentical protein bindingInterproscan
GO:0046498
all species →		Biological ProcessS-adenosylhomocysteine metabolic processInterproscan
GO:0046500
all species →		Biological ProcessS-adenosylmethionine metabolic processInterproscan
GO:0051289
all species →		Biological Processprotein homotetramerizationInterproscan
GO:1901052
all species →		Biological Processsarcosine metabolic processInterproscan
GO:1904047
all species →		Molecular FunctionS-adenosyl-L-methionine bindingInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K00552GNMT; glycine N-methyltransferaseEC:2.1.1.20
Cysteine and methionine metabolismko00270deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g29330.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
38TPM > 0
1Conditions
554.8Max TPM
227.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 38 227.40 554.82

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 554.82
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 432.45
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 419.42
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 392.24
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 344.76
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 329.43
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 321.34
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 307.68
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 303.59
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 299.62
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 298.66
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 295.61
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 277.01
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 262.87
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 255.85
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 253.31
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 251.97
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 249.91
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 219.37
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 217.46
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 215.14
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 211.06
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 204.44
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 189.66
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 188.08
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 176.10
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 173.17
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 164.75
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 145.19
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 131.54
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 130.88
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 126.79
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 117.55
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 97.97
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 93.76
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 91.18
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 66.30
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 57.65
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 0.00

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 Acropora digitifera 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated3g16459.t10.757470969005857
Negatively correlated45g3590.t1-0.726507903571248

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 Acropora digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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