Detailed information of g7610.t1 in Montipora capitata

Genomic Location: Sc0000178:387732...396007
NR annotation: XP_044174607.1, RNA exonuclease 4-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
Q6DEW6RNA exonuclease 4 OS=Xenopus tropicalis OX=8364 GN=rexo4 PE=2 SV=1
Q91560RNA exonuclease 4 OS=Xenopus laevis OX=8355 GN=rexo4 PE=2 SV=2
Q6PAQ4RNA exonuclease 4 OS=Mus musculus OX=10090 GN=Rexo4 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002229 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00929
all species →		RNase_TExonucleaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR047021
all species →		FamilyRNA exonuclease REXO1/REXO3/REXO4-likeInterproscan
IPR013520
all species →		DomainExonuclease, RNase T/DNA polymerase IIIInterproscan
IPR012337
all species →		Homologous_superfamilyRibonuclease H-like superfamilyInterproscan
IPR037431
all species →		DomainRNA exonuclease 4, DEDDh 3'-5' exonuclease domainInterproscan
IPR036397
all species →		Homologous_superfamilyRibonuclease H superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12801
all species →		RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004527
all species →		Molecular Functionexonuclease activityInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006364
all species →		Biological ProcessrRNA processingInterproscan
GO:0008408
all species →		Molecular Function3'-5' exonuclease activityInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan

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
K18327REXO4, REX4; RNA exonuclease 4EC:3.1.-.-
Ribosome biogenesisko03009deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g7610.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
46TPM > 0
3Conditions
56.7Max TPM
22.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 20 25.29 56.67
whole organisms · low pH treatment 15 14 20.27 48.82
whole organisms · extra low pH treatment pH treatment 12 12 19.58 53.01

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 56.67
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 53.60
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 51.09
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 45.17
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 41.86
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 38.64
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 38.58
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 37.56
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 32.11
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 30.13
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 18.16
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 15.74
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 11.99
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 11.68
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 11.00
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 8.59
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 8.44
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 8.10
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 7.06
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 4.95
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 0.00
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 48.82
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 47.21
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 44.91
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 30.83
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 30.23
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 26.11
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 17.16
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 14.37
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 14.13
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 9.36
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 8.54
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 5.68
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 3.67
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 3.10
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 0.00
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 53.01
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 45.20
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 39.41
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 29.89
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 16.23
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 14.61
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 12.62
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 8.99
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 4.82
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 4.49
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 3.09
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 2.57

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 correlated32g10629.t10.964696825885333
Negatively correlated3g5196.t1-0.838843139506654

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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