Detailed information of XP_074636657.1 in Acropora palmata

Genomic Location: NC_133891.1:17634802...17647431
NR annotation: XP_029199167.2, E3 ubiquitin-protein ligase CHFR-like [Acropora millepora]
Species Acropora palmata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q5RF77E3 ubiquitin-protein ligase CHFR OS=Pongo abelii OX=9601 GN=CHFR PE=2 SV=1
Q6P256E3 ubiquitin-protein ligase CHFR OS=Xenopus tropicalis OX=8364 GN=chfr PE=2 SV=1
Q5FWP4E3 ubiquitin-protein ligase CHFR OS=Xenopus laevis OX=8355 GN=chfr PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004876 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13923
all species →		zf-C3HC4_2Zinc finger, C3HC4 type (RING finger)DomainInterproscan
PF00498
all species →		FHAFHA domainFamilyInterproscan
PF17979
all species →		zf-CRDCysteine rich domain with multizinc binding regionsDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR017907
all species →		Conserved_siteZinc finger, RING-type, conserved siteInterproscan
IPR052256
all species →		FamilyE3 ubiquitin-protein ligase CHFRInterproscan
IPR008984
all species →		Homologous_superfamilySMAD/FHA domain superfamilyInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR000253
all species →		DomainForkhead-associated (FHA) domainInterproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR040909
all species →		DomainE3 ubiquitin-protein ligase CHFR, cysteine rich domain with multizinc bindingInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR16079
all species →		UBIQUITIN LIGASE PROTEIN CHFRInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004842
all species →		Molecular Functionubiquitin-protein transferase activityInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006511
all species →		Biological Processubiquitin-dependent protein catabolic processInterproscan
GO:0007093
all species →		Biological Processmitotic cell cycle checkpoint signalingInterproscan
GO:0016567
all species →		Biological Processprotein ubiquitinationInterproscan
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
KOEnzymeEnzyme IDPathwayMap IDSource
K10644CHFR; E3 ubiquitin-protein ligase CHFREC:2.3.2.27
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 XP_074636657.1 across 84 RNA-seq samples of Acropora palmata. 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.

84Samples
52TPM > 0
2Conditions
20.7Max TPM
6.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
all_coral_tissue · exposed 46 28 5.52 17.65
all_coral_tissue · baseline 38 24 8.39 20.75

Per sample · hover a bar for the full sample record

Show the sample table (84 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR8800036 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 17.65
SRR8800068 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 17.01
SRR8800100 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 13.86
SRR8800051 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 12.88
SRR8800097 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 12.72
SRR8800038 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 12.16
SRR8800080 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 12.02
SRR8800099 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 11.84
SRR8800079 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 10.94
SRR8800044 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 10.23
SRR8800053 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 9.76
SRR8800083 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 9.39
SRR8800077 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 8.75
SRR8800073 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 8.64
SRR8800071 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 8.55
SRR8800045 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 8.52
SRR8800095 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 8.09
SRR8800060 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 7.92
SRR8800033 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 7.78
SRR8800093 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 7.61
SRR8800062 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 6.87
SRR8800063 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 6.30
SRR8800058 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 6.21
SRR8800047 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 5.29
SRR8800065 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 4.71
SRR8800107 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 3.04
SRR8800087 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 2.82
SRR8800026 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 2.35
SRR8800027 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800028 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800029 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800034 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800039 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800040 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800042 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800056 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800061 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800066 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800075 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800086 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800088 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800089 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800091 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800092 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800094 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800105 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800098 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 20.75
SRR8800041 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 19.73
SRR8800043 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 19.59
SRR8800057 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 18.23
SRR8800076 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 16.42
SRR8800069 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 16.34
SRR8800081 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 16.12
SRR8800074 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 15.83
SRR8800048 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 14.57
SRR8800037 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 14.07
SRR8800078 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 13.79
SRR8800050 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 13.42
SRR8800067 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 13.29
SRR8800072 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 12.81
SRR8800049 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 12.36
SRR8800096 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 11.97
SRR8800103 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 11.08
SRR8800102 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 11.01
SRR8800070 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 10.36
SRR8800109 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 10.19
SRR8800101 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 9.06
SRR8800064 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 7.14
SRR8800084 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 5.49
SRR8800085 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 5.39
SRR8800030 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800031 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800032 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800035 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800046 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800052 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800054 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800055 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800059 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800082 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800090 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800104 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800106 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800108 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00

Source: CnidoSite RNA-seq expression matrices (APALM_TPM, StringTie quantification over 84 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 Acropora palmata 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 correlated33XP_074639008.10.916683033153876
Negatively correlated3XP_074625347.1-0.536101538811323

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 Acropora palmata, 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.

DNA methylation (bisulphite samples)

SampleMethylation profile
Polyp_Underside_Control_2open
Polyp_Underside_Control_3open
Polyp_Underside_Treatment_1open
Polyp_Upperside_Control_1open
Polyp_Upperside_Treatment_3open
Polyp_Upperside_Treatment_4open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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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