Detailed information of XP_068732811.1 in Montipora capricornis

Genomic Location: chr13:10605384...10613137
NR annotation: XP_029210292.1, histone H3.3-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q803H4Histone H3-like centromeric protein A OS=Danio rerio OX=7955 GN=cenpa PE=1 SV=1
P90543Histone H3 OS=Euplotes crassus OX=5936 PE=3 SV=3
Q7RXR3Histone H3-like centromeric protein hH3v OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) OX=367110 GN=hH3v PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000363 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00125
all species →		HistoneCore histone H2A/H2B/H3/H4DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR009072
all species →		Homologous_superfamilyHistone-foldInterproscan
IPR000164
all species →		FamilyHistone H3/CENP-AInterproscan
IPR007125
all species →		DomainHistone H2A/H2B/H3Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45810
all species →		HISTONE H3.2Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0046982
all species →		Molecular Functionprotein heterodimerization activityInterproscan
GO:0000786
all species →		Cellular ComponentnucleosomeInterproscan
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0030527
all species →		Molecular Functionstructural constituent of chromatinInterproscan

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
K11495CENPA; histone H3-like centromeric protein A-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 XP_068732811.1 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
28TPM > 0
1Conditions
96.2Max TPM
46.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 28 46.14 96.24

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12786897 Polyps Polyps OA3 day0 not recorded SRP199550 96.24
SRR12786896 Polyps Polyps OA3 day0 not recorded SRP199550 91.33
SRR12786898 Polyps Polyps OA3 day0 not recorded SRP199550 80.04
SRR12959182 Polyps Polyps E3 day0 not recorded SRP199550 79.14
SRR12959184 Polyps Polyps E3 day0 not recorded SRP199550 77.08
SRR12959201 Polyps Polyps E3 day15 not recorded SRP199550 74.05
SRR12959202 Polyps Polyps E3 day15 not recorded SRP199550 71.97
SRR12959183 Polyps Polyps E3 day0 not recorded SRP199550 71.05
SRR12959203 Polyps Polyps E3 day15 not recorded SRP199550 70.46
SRR12710857 Polyps Polyps OA3 day9 not recorded SRP199550 66.01
SRR12959214 Polyps Polyps E3 day9 not recorded SRP199550 65.89
SRR12959230 Polyps Polyps E3 day3 not recorded SRP199550 61.77
SRR12710855 Polyps Polyps OA3 day9 not recorded SRP199550 60.49
SRR12710858 Polyps Polyps OA3 day9 not recorded SRP199550 59.75
SRR12959215 Polyps Polyps E3 day9 not recorded SRP199550 54.47
SRR12959216 Polyps Polyps E3 day9 not recorded SRP199550 52.63
SRR12959189 Polyps Polyps E3 day21 not recorded SRP199550 52.47
SRR12959190 Polyps Polyps E3 day21 not recorded SRP199550 50.35
SRR12710846 Polyps Polyps OA3 day3 not recorded SRP199550 47.91
SRR12710847 Polyps Polyps OA3 day3 not recorded SRP199550 47.43
SRR12710848 Polyps Polyps OA3 day3 not recorded SRP199550 47.03
SRR12959188 Polyps Polyps E3 day21 not recorded SRP199550 44.40
SRR12959229 Polyps Polyps E3 day3 not recorded SRP199550 43.74
SRR12904783 Polyps Polyps not recorded not recorded SRP199550 42.29
SRR27940191 Polyps Polyps not recorded not recorded SRP199550 41.54
SRR27940193 Polyps Polyps not recorded not recorded SRP199550 40.67
SRR12904782 Polyps Polyps not recorded not recorded SRP199550 36.74
SRR12904781 Polyps Polyps not recorded not recorded SRP199550 34.12
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
SRR12959227 Polyps Polyps E3 day3 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated28XP_068738297.10.946047081051335
Negatively correlated3XP_068724527.1-0.482782780959881

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.

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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