Detailed information of g22820.t1 in Montipora capitata

Genomic Location: Sc0001853:17513...20245
NR annotation: XP_029196007.2, cytochrome b-c1 complex subunit Rieske, mitochondrial-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
Q9VQ29Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Drosophila melanogaster OX=7227 GN=RFeSP PE=1 SV=3
P13272Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Bos taurus OX=9913 GN=UQCRFS1 PE=1 SV=3
P20788Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Rattus norvegicus OX=10116 GN=Uqcrfs1 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008193 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02921
all species →		UCR_TMUbiquinol cytochrome reductase transmembrane regionFamilyInterproscan
PF00355
all species →		RieskeRieske [2Fe-2S] domainDomainInterproscan
PF09165
all species →		Ubiq-Cytc-red_NUbiquinol-cytochrome c reductase 8 kDa, N-terminalDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR037008
all species →		Homologous_superfamilyCytochrome bc1 complex subunit Rieske, transmembrane domain superfamilyInterproscan
IPR004192
all species →		DomainCytochrome b-c1 complex subunit Rieske, transmembrane domainInterproscan
IPR017941
all species →		DomainRieske [2Fe-2S] iron-sulphur domainInterproscan
IPR036922
all species →		Homologous_superfamilyRieske [2Fe-2S] iron-sulphur domain superfamilyInterproscan
IPR005805
all species →		DomainRieske iron-sulphur protein, C-terminalInterproscan
IPR015248
all species →		DomainUbiquinol-cytochrome c reductase iron-sulphur subunit, N-terminalInterproscan
IPR014349
all species →		FamilyRieske iron-sulphur proteinInterproscan
IPR006317
all species →		DomainUbiquinol-cytochrome c reductase, iron-sulphur subunitInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10134
all species →		CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008121
all species →		Molecular Functionubiquinol-cytochrome-c reductase activityInterproscan
GO:0051537
all species →		Molecular Function2 iron, 2 sulfur cluster bindingInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0005750
all species →		Cellular Componentobsolete mitochondrial respiratory chain complex IIIInterproscan
GO:0006122
all species →		Biological Processmitochondrial electron transport, ubiquinol to cytochrome cInterproscan
GO:0016491
all species →		Molecular Functionoxidoreductase activityInterproscan

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
K00411UQCRFS1, RIP1, petA; ubiquinol-cytochrome c reductase iron-sulfur subunitEC:7.1.1.8
Non-alcoholic fatty liver diseaseko04932deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g22820.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
732.4Max TPM
409.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 417.03 701.56
whole organisms · low pH treatment 15 15 400.35 732.39
whole organisms · extra low pH treatment pH treatment 12 12 405.87 653.49

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 701.56
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 595.14
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 559.10
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 556.74
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 544.62
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 505.06
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 439.37
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 410.09
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 404.24
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 388.75
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 370.50
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 368.05
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 366.11
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 363.32
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 347.18
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 341.16
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 337.54
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 316.54
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 312.54
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 292.32
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 237.61
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 732.39
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 612.31
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 517.38
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 474.70
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 381.30
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 371.24
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 363.03
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 359.62
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 354.20
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 336.00
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 326.12
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 306.71
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 304.36
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 301.88
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 263.95
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 653.49
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 642.22
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 600.48
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 403.70
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 392.02
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 371.73
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 353.53
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 324.54
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 297.90
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 292.78
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 292.50
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 245.55

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 correlated12g881.t10.94275967383333
Negatively correlated31g799.t1-0.91998918522353

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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