Detailed information of g5710.t1 in Montipora capitata

Genomic Location: Sc0000116:274191...276718
NR annotation: XP_029179676.1, pituitary homeobox 2-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9R0W1Pituitary homeobox 2 OS=Rattus norvegicus OX=10116 GN=Pitx2 PE=2 SV=1
Q6QU75Pituitary homeobox 3 OS=Danio rerio OX=7955 GN=pitx3 PE=2 SV=1
Q9I8K3Pituitary homeobox 3 OS=Xenopus laevis OX=8355 GN=pitx3 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008699 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00046
all species →		HomeodomainHomeodomainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001356
all species →		DomainHomeobox domainInterproscan
IPR017970
all species →		Conserved_siteHomeobox, conserved siteInterproscan
IPR009057
all species →		Homologous_superfamilyHomeobox-like domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45882
all species →		PITUITARY HOMEOBOX HOMOLOG PTX1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0000981
all species →		Molecular FunctionDNA-binding transcription factor activity, RNA polymerase II-specificInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0000978
all species →		Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:0009653
all species →		Biological Processanatomical structure morphogenesisInterproscan

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
K09357PITX3; paired-like homeodomain transcription factor 3-Transcription factorsko03000deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g5710.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples
48TPM > 0
3Conditions
1,042.2Max TPM
263.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 285.74 1,042.23
whole organisms · low pH treatment 15 15 243.37 991.12
whole organisms · extra low pH treatment pH treatment 12 12 248.58 838.63

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 1,042.23
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 930.91
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 866.91
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 537.41
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 493.14
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 444.33
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 422.84
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 417.08
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 351.48
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 328.06
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 40.62
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 35.44
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 24.58
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 14.86
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 11.28
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 10.04
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 9.89
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 9.58
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 4.88
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 4.17
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 0.73
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 991.12
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 880.79
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 829.63
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 288.53
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 287.65
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 249.66
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 32.96
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 29.33
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 24.48
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 8.79
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 7.59
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 7.52
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 5.10
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 4.37
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 2.97
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 838.63
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 824.62
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 413.76
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 412.73
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 406.06
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 29.84
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 28.38
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 7.82
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 7.03
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 6.42
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 4.00
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 3.70

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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 capitata 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 correlated40g5461.t10.991130528778124
Negatively correlated9g11563.t1-0.898819476112134

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 capitata, 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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