Detailed information of g19641.t1 in Acropora digitifera

Genomic Location: chr9Alt:9121285...9146753
NR annotation: XP_044174240.1, DNA topoisomerase 2-alpha-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
P41515DNA topoisomerase 2-alpha OS=Cricetulus griseus OX=10029 GN=TOP2A PE=2 SV=1
Q01320DNA topoisomerase 2-alpha OS=Mus musculus OX=10090 GN=Top2a PE=1 SV=2
O46374DNA topoisomerase 2-alpha OS=Sus scrofa OX=9823 GN=TOP2A PE=2 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00204
all species →		DNA_gyraseBDNA gyrase BDomainInterproscan
PF01751
all species →		ToprimToprim domainFamilyInterproscan
PF00521
all species →		DNA_topoisoIVDNA gyrase/topoisomerase IV, subunit AFamilyInterproscan
PF02518
all species →		HATPase_cHistidine kinase-, DNA gyrase B-, and HSP90-like ATPaseDomainInterproscan
PF16898
all species →		TOPRIM_CC-terminal associated domain of TOPRIMFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013758
all species →		Homologous_superfamilyDNA topoisomerase, type IIA, domain A, alpha-betaInterproscan
IPR050634
all species →		FamilyDNA Topoisomerase II EnzymeInterproscan
IPR034157
all species →		DomainDNA topoisomerase 2, TOPRIM domainInterproscan
IPR013757
all species →		Homologous_superfamilyDNA topoisomerase, type IIA, alpha-helical domain superfamilyInterproscan
IPR001154
all species →		FamilyDNA topoisomerase II, eukaryotic-typeInterproscan
IPR002205
all species →		DomainDNA topoisomerase, type IIA, domain AInterproscan
IPR036890
all species →		Homologous_superfamilyHistidine kinase/HSP90-like ATPase superfamilyInterproscan
IPR018522
all species →		Conserved_siteDNA topoisomerase, type IIA, conserved siteInterproscan
IPR013760
all species →		Homologous_superfamilyDNA topoisomerase, type IIA-like domain superfamilyInterproscan
IPR013506
all species →		DomainDNA topoisomerase, type IIA, subunit B, domain 2Interproscan
IPR006171
all species →		DomainTOPRIM domainInterproscan
IPR001241
all species →		FamilyDNA topoisomerase, type IIAInterproscan
IPR003594
all species →		DomainHistidine kinase/HSP90-like ATPaseInterproscan
IPR013759
all species →		Homologous_superfamilyDNA topoisomerase, type IIA, subunit B, C-terminalInterproscan
IPR014721
all species →		Homologous_superfamilySmall ribosomal subunit protein uS5 domain 2-type fold, subgroupInterproscan
IPR020568
all species →		Homologous_superfamilyRibosomal protein uS5 domain 2-type superfamilyInterproscan
IPR031660
all species →		DomainC-terminal associated domain of TOPRIMInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10169
all species →		DNA TOPOISOMERASE/GYRASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0003918
all species →		Molecular FunctionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activityInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0006259
all species →		Biological ProcessDNA metabolic processInterproscan
GO:0006265
all species →		Biological ProcessDNA topological changeInterproscan
GO:0000712
all species →		Biological Processresolution of meiotic recombination intermediatesInterproscan
GO:0000819
all species →		Biological Processsister chromatid segregationInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan

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
K03164TOP2; DNA topoisomerase IIEC:5.6.2.2
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 g19641.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
68.7Max TPM
51.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 51.39 68.70

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 68.70
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 64.97
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 64.24
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 63.78
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 61.92
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 60.88
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 60.73
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 60.20
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 59.60
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 59.08
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 57.05
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 55.91
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 55.83
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 55.27
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 55.06
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 54.59
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 53.62
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 53.17
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 52.24
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 50.59
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 49.76
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 48.57
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 48.26
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 47.99
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 47.60
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 47.18
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 47.00
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 46.75
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 46.72
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 45.56
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 44.98
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 44.38
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 44.26
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 43.89
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 40.29
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 39.93
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 38.55
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 37.00
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 28.15

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 correlated29g7123.t10.843920712624127
Negatively correlated18g7371.t1-0.744509220387943

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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