Detailed information of g13776.t1 in Montipora capitata

Genomic Location: Sc0000484:155861...163678
NR annotation: XP_044172182.1, regulator of nonsense transcripts 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
A2AT37Regulator of nonsense transcripts 2 OS=Mus musculus OX=10090 GN=Upf2 PE=1 SV=1
Q9HAU5Regulator of nonsense transcripts 2 OS=Homo sapiens OX=9606 GN=UPF2 PE=1 SV=1
F4IUX6Regulator of nonsense transcripts UPF2 OS=Arabidopsis thaliana OX=3702 GN=UPF2 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003459 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02854
all species →		MIF4GMIF4G domainRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR039762
all species →		FamilyNonsense-mediated mRNA decay protein Nmd2/UPF2Interproscan
IPR003890
all species →		DomainMIF4G-like, type 3Interproscan
IPR016024
all species →		Homologous_superfamilyArmadillo-type foldInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12839
all species →		NONSENSE-MEDIATED MRNA DECAY PROTEIN 2 UP-FRAMESHIFT SUPPRESSOR 2Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000184
all species →		Biological Processnuclear-transcribed mRNA catabolic process, nonsense-mediated decayInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0005844
all species →		Cellular Componentobsolete polysomeInterproscan
GO:0035145
all species →		Cellular Componentexon-exon junction complexInterproscan
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0005515
all species →		Molecular Functionprotein 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
No KEGG orthology assignment for g13776.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g13776.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
515.7Max TPM
166.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 157.56 515.74
whole organisms · low pH treatment 15 15 178.95 409.11
whole organisms · extra low pH treatment pH treatment 12 12 166.91 346.91

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 515.74
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 287.92
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 273.77
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 262.04
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 246.24
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 242.81
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 230.95
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 223.25
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 212.11
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 126.98
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 107.03
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 106.84
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 73.60
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 71.03
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 68.20
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 57.36
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 48.82
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 48.02
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 43.88
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 40.13
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 22.10
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 409.11
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 306.93
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 301.20
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 300.77
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 279.40
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 197.20
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 186.86
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 175.19
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 136.73
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 123.07
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 101.85
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 65.83
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 38.38
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 31.40
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 30.33
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 346.91
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 316.76
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 269.66
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 242.43
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 189.00
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 160.75
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 137.28
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 132.46
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 75.98
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 53.26
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 44.08
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 34.31

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 correlated24g524.t10.973279829834883
Negatively correlated3g11255.t1-0.886900858232759

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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