Detailed information of g8988.t1 in Acropora digitifera

Genomic Location: chr4Alt:15301837...15307685
NR annotation: XP_029184392.1, E3 ubiquitin-protein ligase ZNRF2-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q71FD5E3 ubiquitin-protein ligase ZNRF2 OS=Mus musculus OX=10090 GN=Znrf2 PE=1 SV=1
F1MM41E3 ubiquitin-protein ligase ZNRF1 OS=Bos taurus OX=9913 GN=ZNRF1 PE=3 SV=2
Q8ND25E3 ubiquitin-protein ligase ZNRF1 OS=Homo sapiens OX=9606 GN=ZNRF1 PE=1 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13639
all species →		zf-RING_2Ring finger domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR051878
all species →		FamilyZNRF ubiquitin-protein ligaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46661
all species →		E3 UBIQUITIN-PROTEIN LIGASE ZNRF1-LIKE PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0043161
all species →		Biological Processproteasome-mediated ubiquitin-dependent protein catabolic processInterproscan
GO:0043231
all species →		Cellular Componentintracellular membrane-bounded organelleInterproscan
GO:0061630
all species →		Molecular Functionubiquitin protein ligase activityInterproscan
GO:0070936
all species →		Biological Processprotein K48-linked ubiquitinationInterproscan

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
K10694ZNRF1_2; E3 ubiquitin-protein ligase ZNRF1/2EC: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 g8988.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
39TPM > 0
1Conditions
140.6Max TPM
87.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 87.59 140.64

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 140.64
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 111.12
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 107.07
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 106.51
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 105.38
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 105.26
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 102.70
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 99.06
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 98.62
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 96.59
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 96.54
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 94.21
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 92.51
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 92.18
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 91.64
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 90.32
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 90.15
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 89.94
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 87.09
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 86.88
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 86.37
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 85.60
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 84.26
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 83.20
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 82.19
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 81.69
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 78.34
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 77.25
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 76.76
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 75.68
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 73.79
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 73.43
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 72.12
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 70.42
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 69.92
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 68.55
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 67.84
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 65.95
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 58.20

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 digitifera 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 correlated26g3344.t10.836661105203779
Negatively correlated11g18496.t1-0.780431411722351

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 digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion
DNase-seq (DHS)WholeAnimal1Distal Intergenic 1

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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 →
TOP