Detailed information of g21856.t1 in Montipora capitata

Genomic Location: Sc0001521:8688...18091
NR annotation: XP_029211460.2, DNA replication licensing factor MCM3-like isoform X2 [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
P49739Maternal DNA replication licensing factor mcm3 OS=Xenopus laevis OX=8355 GN=mmcm3 PE=1 SV=2
Q7ZXZ0Zygotic DNA replication licensing factor mcm3 OS=Xenopus laevis OX=8355 GN=zmcm3 PE=1 SV=1
P25206DNA replication licensing factor MCM3 OS=Mus musculus OX=10090 GN=Mcm3 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003857 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00493
all species →		MCMMCM P-loop domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR031327
all species →		FamilyMini-chromosome maintenance proteinInterproscan
IPR008046
all species →		FamilyDNA replication licensing factor Mcm3Interproscan
IPR003593
all species →		DomainAAA+ ATPase domainInterproscan
IPR001208
all species →		DomainMCM domainInterproscan
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR018525
all species →		Conserved_siteMini-chromosome maintenance, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11630
all species →		DNA REPLICATION LICENSING FACTOR MCM FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000727
all species →		Biological Processdouble-strand break repair via break-induced replicationInterproscan
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0003697
all species →		Molecular Functionsingle-stranded DNA bindingInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006271
all species →		Biological ProcessDNA strand elongation involved in DNA replicationInterproscan
GO:0017116
all species →		Molecular Functionsingle-stranded DNA helicase activityInterproscan
GO:0032508
all species →		Biological ProcessDNA duplex unwindingInterproscan
GO:0042555
all species →		Cellular ComponentMCM complexInterproscan
GO:1902975
all species →		Biological Processmitotic DNA replication initiationInterproscan
GO:0006270
all species →		Biological ProcessDNA replication initiationInterproscan
GO:0016887
all species →		Molecular FunctionATP hydrolysis activityInterproscan
GO:0006260
all species →		Biological ProcessDNA replicationInterproscan

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
No KEGG orthology assignment for g21856.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g21856.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
93.4Max TPM
48.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 48.75 86.05
whole organisms · low pH treatment 15 15 50.38 93.45
whole organisms · extra low pH treatment pH treatment 12 12 47.10 73.95

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 86.05
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 81.01
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 78.94
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 63.02
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 62.40
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 61.73
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 58.26
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 57.76
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 54.97
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 52.01
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 50.05
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 49.42
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 48.06
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 39.15
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 36.93
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 32.04
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 29.79
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 25.63
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 21.51
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 17.90
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 17.08
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 93.45
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 82.59
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 65.01
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 63.87
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 59.44
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 57.34
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 56.43
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 54.38
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 48.38
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 34.83
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 34.58
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 31.28
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 28.67
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 28.46
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 16.96
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 73.95
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 61.48
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 61.38
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 58.31
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 55.70
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 55.23
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 45.93
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 41.70
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 37.33
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 35.33
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 19.79
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 19.01

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 correlated15g16683.t10.928644662576781
Negatively correlated4g27310.t1-0.858469062681579

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 →
TOP