Detailed information of g15353.t1 in Montipora capitata

Genomic Location: Sc0000601:8620...15575
NR annotation: XP_020626141.1, NEDD8-conjugating enzyme UBE2F-like [Orbicella faveolata]
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
Q5ZKX6NEDD8-conjugating enzyme UBE2F OS=Gallus gallus OX=9031 GN=UBE2F PE=2 SV=1
Q969M7NEDD8-conjugating enzyme UBE2F OS=Homo sapiens OX=9606 GN=UBE2F PE=1 SV=1
Q1RMW1NEDD8-conjugating enzyme UBE2F OS=Bos taurus OX=9913 GN=UBE2F PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0009302 (this species only) · gene tree & orthology
Ubiquitin familyE2|UBC|UBC · all ubiquitin genes in this species
Ubiquitin familyUBD|UBC-like|UBC · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00179
all species →		UQ_conUbiquitin-conjugating enzymeDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000608
all species →		DomainUbiquitin-conjugating enzyme E2Interproscan
IPR016135
all species →		Homologous_superfamilyUbiquitin-conjugating enzyme/RWD-likeInterproscan
IPR050113
all species →		FamilyUbiquitin-conjugating enzymeInterproscan
IPR023313
all species →		Active_siteUbiquitin-conjugating enzyme, active siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24067
all species →		UBIQUITIN-CONJUGATING ENZYME E2Interproscan

 Gene Ontology
No Gene Ontology signature was recorded for g15353.t1 in Montipora capitata.
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
K10687UBE2F; ubiquitin-conjugating enzyme E2 FEC:2.3.2.34
Ubiquitin systemko04121deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g15353.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
199.9Max TPM
91.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 89.72 192.69
whole organisms · low pH treatment 15 15 94.65 199.90
whole organisms · extra low pH treatment pH treatment 12 12 91.20 197.36

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 192.69
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 173.96
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 168.81
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 158.80
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 131.16
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 127.40
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 127.28
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 121.04
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 113.47
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 96.08
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 86.82
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 63.06
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 60.84
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 44.66
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 41.20
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 39.41
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 36.37
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 29.43
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 26.86
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 26.00
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 18.80
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 199.90
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 172.58
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 131.39
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 124.12
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 111.54
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 111.26
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 93.55
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 87.06
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 74.35
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 73.98
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 69.05
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 54.00
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 41.99
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 41.89
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 33.11
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 197.36
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 168.86
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 120.13
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 108.35
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 103.04
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 90.56
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 79.80
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 63.72
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 61.77
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 40.33
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 33.41
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 27.08

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 correlated26g596.t10.954476651143877
Negatively correlated3g16172.t1-0.827713370955899

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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