Detailed information of g14622.t1 in Acropora digitifera

Genomic Location: chr7Alt:941443...950748
NR annotation: XP_029184703.2, lysine-specific demethylase 4B-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
Q8VCD7Lysine-specific demethylase 4C OS=Mus musculus OX=10090 GN=Kdm4c PE=1 SV=1
Q9H3R0Lysine-specific demethylase 4C OS=Homo sapiens OX=9606 GN=KDM4C PE=1 SV=2
Q8BW72Lysine-specific demethylase 4A OS=Mus musculus OX=10090 GN=Kdm4a PE=1 SV=3
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF18104
all species →		Tudor_2Jumonji domain-containing protein 2A Tudor domainDomainInterproscan
PF02375
all species →		JmjNjmjN domainFamilyInterproscan
PF13832
all species →		zf-HC5HC2H_2PHD-zinc-finger like domainDomainInterproscan
PF13831
all species →		PHD_2PHD-fingerFamilyInterproscan
PF02373
all species →		JmjCJmjC domain, hydroxylaseDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR040477
all species →		DomainLysine-specific demethylase 4-like, Tudor domainInterproscan
IPR003349
all species →		DomainJmjN domainInterproscan
IPR001965
all species →		DomainZinc finger, PHD-typeInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR003347
all species →		DomainJmjC domainInterproscan
IPR034732
all species →		DomainExtended PHD (ePHD) domainInterproscan
IPR002999
all species →		DomainTudor domainInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10694
all species →		LYSINE-SPECIFIC DEMETHYLASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000785
all species →		Cellular ComponentchromatinInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006338
all species →		Biological Processchromatin remodelingInterproscan
GO:0010468
all species →		Biological Processregulation of gene expressionInterproscan
GO:0032452
all species →		Molecular Functionhistone demethylase activityInterproscan
GO:0032454
all species →		Molecular Functionhistone H3K9 demethylase activityInterproscan

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
K06709KDM4, JMJD2, JHDM3; [histone H3]-trimethyl-L-lysine9/36 demethylaseEC:1.14.11.66
EC:1.14.11.69
Chromosome and associated proteinsko03036deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g14622.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
39TPM > 0
1Conditions
62.0Max TPM
38.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 38.07 61.99

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 61.99
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 54.55
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 48.08
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 43.49
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 43.21
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 42.65
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 41.83
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 41.79
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 41.63
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 41.03
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 41.01
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 40.94
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 40.93
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 40.86
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 40.58
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 40.47
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 40.46
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 40.05
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 39.95
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 39.89
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 37.96
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 37.81
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 37.45
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 36.63
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 35.74
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 34.98
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 34.98
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 33.32
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 33.14
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 32.92
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 32.92
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 32.81
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 31.75
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 30.70
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 29.84
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 28.90
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 28.41
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 26.55
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 22.69

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 correlated15g16679.t10.810369596886966
Negatively correlated12g5200.t1-0.688511883751051

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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