Detailed information of XP_029204788.1 in Acropora millepora

Genomic Location: NC_058073.1:13146706...13158317
NR annotation: XP_029204788.1, histone deacetylase 11-like isoform X1 [Acropora millepora]
Species Acropora millepora · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q96DB2Histone deacetylase 11 OS=Homo sapiens OX=9606 GN=HDAC11 PE=1 SV=1
Q9GKU5Histone deacetylase 11 OS=Macaca fascicularis OX=9541 GN=HDAC11 PE=2 SV=2
Q91WA3Histone deacetylase 11 OS=Mus musculus OX=10090 GN=Hdac11 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006091 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00850
all species →		Hist_deacetylHistone deacetylase domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR023801
all species →		DomainHistone deacetylase domainInterproscan
IPR050284
all species →		FamilyHistone deacetylase and polyamine deacetylaseInterproscan
IPR037138
all species →		Homologous_superfamilyHistone deacetylase domain superfamilyInterproscan
IPR044150
all species →		DomainHistone deacetylase 11Interproscan
IPR000286
all species →		FamilyHistone deacetylase familyInterproscan
IPR023696
all species →		Homologous_superfamilyUreohydrolase domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10625
all species →		HISTONE DEACETYLASE HDAC1-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000118
all species →		Cellular Componenthistone deacetylase complexInterproscan
GO:0004407
all species →		Molecular Functionhistone deacetylase activityInterproscan
GO:0016575
all species →		Biological Processobsolete histone deacetylationInterproscan

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
K11418HDAC11; histone deacetylase 11EC:3.5.1.98
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_029204788.1 across 54 RNA-seq samples of Acropora millepora. 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.

54Samples
25TPM > 0
2Conditions
1,655.2Max TPM
363.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole larvae 30 17 548.08 1,655.17
branch 24 8 132.82 604.94

Per sample · hover a bar for the full sample record

Show the sample table (54 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR1929615 whole larvae whole larvae adult not recorded SRP056536 1,655.17
SRR1929616 whole larvae whole larvae adult not recorded SRP056536 1,428.06
SRR1929623 whole larvae whole larvae adult not recorded SRP056536 1,357.71
SRR1929617 whole larvae whole larvae adult not recorded SRP056536 1,305.40
SRR1929609 whole larvae whole larvae adult not recorded SRP056536 1,280.16
SRR1929627 whole larvae whole larvae adult not recorded SRP056536 1,130.13
SRR1929612 whole larvae whole larvae adult not recorded SRP056536 1,034.13
SRR1929634 whole larvae whole larvae adult not recorded SRP056536 1,028.39
SRR1929614 whole larvae whole larvae adult not recorded SRP056536 807.75
SRR1929633 whole larvae whole larvae adult not recorded SRP056536 801.51
SRR1929605 whole larvae whole larvae adult not recorded SRP056536 686.09
SRR1929620 whole larvae whole larvae adult not recorded SRP056536 684.64
SRR1929606 whole larvae whole larvae adult not recorded SRP056536 681.28
SRR1929622 whole larvae whole larvae adult not recorded SRP056536 677.75
SRR1929630 whole larvae whole larvae adult not recorded SRP056536 676.90
SRR1929628 whole larvae whole larvae adult not recorded SRP056536 623.03
SRR1929626 whole larvae whole larvae adult not recorded SRP056536 584.40
SRR1929607 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929608 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929610 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929611 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929613 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929618 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929619 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929621 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929624 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929625 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929629 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929631 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929632 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929585 branch branch adult not recorded SRP056536 604.94
SRR1929595 branch branch adult not recorded SRP056536 521.26
SRR1929586 branch branch adult not recorded SRP056536 431.00
SRR1929590 branch branch adult not recorded SRP056536 401.10
SRR1929598 branch branch adult not recorded SRP056536 390.87
SRR1929581 branch branch adult not recorded SRP056536 289.71
SRR1929596 branch branch adult not recorded SRP056536 275.22
SRR1929597 branch branch adult not recorded SRP056536 273.62
SRR1929582 branch branch adult not recorded SRP056536 0.00
SRR1929583 branch branch adult not recorded SRP056536 0.00
SRR1929584 branch branch adult not recorded SRP056536 0.00
SRR1929587 branch branch adult not recorded SRP056536 0.00
SRR1929588 branch branch adult not recorded SRP056536 0.00
SRR1929589 branch branch adult not recorded SRP056536 0.00
SRR1929591 branch branch adult not recorded SRP056536 0.00
SRR1929592 branch branch adult not recorded SRP056536 0.00
SRR1929593 branch branch adult not recorded SRP056536 0.00
SRR1929594 branch branch adult not recorded SRP056536 0.00
SRR1929599 branch branch adult not recorded SRP056536 0.00
SRR1929600 branch branch adult not recorded SRP056536 0.00
SRR1929601 branch branch adult not recorded SRP056536 0.00
SRR1929602 branch branch adult not recorded SRP056536 0.00
SRR1929603 branch branch adult not recorded SRP056536 0.00
SRR1929604 branch branch adult not recorded SRP056536 0.00

Source: CnidoSite RNA-seq expression matrices (AMILL_TPM, StringTie quantification over 54 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 millepora 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 correlated0not in this network-
Negatively correlated11XP_044173720.1-0.483669946332723

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 millepora, 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.

DatasetTissue / stageCellsCell typesThis geneMarker of
AMILL_whole_adultWhole adults · Adult tissues/organs25,16427not in this dataset–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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.

DNA methylation (bisulphite samples)

SampleMethylation profile
planulaopen

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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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