Detailed information of KXJ29136.1 in Exaiptasia diaphana

Genomic Location: LJWW01000007.1:698792...701932
NR annotation: XP_020913178.1, E3 ubiquitin-protein ligase RNF34 [Exaiptasia diaphana]
Species Exaiptasia diaphana · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q969K3E3 ubiquitin-protein ligase RNF34 OS=Homo sapiens OX=9606 GN=RNF34 PE=1 SV=1
Q5NVC7E3 ubiquitin-protein ligase RNF34 OS=Pongo abelii OX=9601 GN=RNF34 PE=2 SV=2
Q8WZ73E3 ubiquitin-protein ligase rififylin OS=Homo sapiens OX=9606 GN=RFFL PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008710 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13920
all species →		zf-C3HC4_3Zinc finger, C3HC4 type (RING finger)DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR051728
all species →		FamilyRING-FYVE domain-containing E3 ubiquitin-protein ligaseInterproscan
IPR017455
all species →		DomainZinc finger, FYVE-relatedInterproscan
IPR036361
all species →		Homologous_superfamilySAP domain superfamilyInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14879
all species →		CASPASE REGULATOR, RING FINGER DOMAIN-CONTAININGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0043161
all species →		Biological Processproteasome-mediated ubiquitin-dependent protein catabolic processInterproscan
GO:0061630
all species →		Molecular Functionubiquitin protein ligase activityInterproscan
GO:0070936
all species →		Biological Processprotein K48-linked ubiquitinationInterproscan
GO:1902042
all species →		Biological Processnegative regulation of extrinsic apoptotic signaling pathway via death domain receptorsInterproscan
GO:2001271
all species →		Biological Processobsolete negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosisInterproscan

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
K20804RNF34; E3 ubiquitin-protein ligase RNF34EC:2.3.2.31
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 KXJ29136.1 across 72 RNA-seq samples of Exaiptasia diaphana. 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.

72Samples
66TPM > 0
2Conditions
53.4Max TPM
29.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole animal · aposymbiotic 36 32 26.13 49.92
whole animal · symbiotic 36 34 33.27 53.43

Per sample · hover a bar for the full sample record

Show the sample table (72 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6202358 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 49.92
SRR6202234 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 41.92
SRR6202260 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 35.43
SRR6202241 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 35.15
SRR6202205 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 34.85
SRR6202209 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 32.57
SRR6202261 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 32.00
SRR6202242 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 31.53
SRR6202258 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 31.07
SRR6202235 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 31.03
SRR6202212 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 30.15
SRR6202233 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 29.52
SRR6202203 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 29.45
SRR6202259 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 29.01
SRR6202211 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 28.91
SRR6202238 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 28.69
SRR6202346 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 28.59
SRR6202204 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 28.42
SRR6202363 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 27.98
SRR6202206 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 27.95
SRR6202236 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 27.14
SRR6202255 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 27.05
SRR6202257 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 26.88
SRR6202208 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 26.69
SRR6202256 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 26.09
SRR6202237 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 26.06
SRR6202207 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 25.96
SRR6202239 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 25.15
SRR6202254 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 24.21
SRR6202210 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 23.63
SRR6202240 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 23.31
SRR6202343 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 14.26
SRR6202344 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202345 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202357 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202364 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202349 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 53.43
SRR6202308 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 48.11
SRR6202348 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 43.06
SRR6202347 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 41.71
SRR6202283 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 41.63
SRR6202284 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 38.41
SRR6202340 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 38.21
SRR6202307 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 37.80
SRR6202262 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 37.07
SRR6202285 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 36.73
SRR6202305 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 36.24
SRR6202282 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 35.67
SRR6202341 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 35.61
SRR6202339 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 35.35
SRR6202281 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 35.33
SRR6202306 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 35.19
SRR6202309 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 35.09
SRR6202280 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 34.86
SRR6202356 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 33.36
SRR6202263 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 33.34
SRR6202350 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 33.31
SRR6202351 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 33.15
SRR6202303 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 33.03
SRR6202354 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 32.49
SRR6202304 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 32.09
SRR6202352 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 31.33
SRR6202279 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 31.20
SRR6202338 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 31.04
SRR6202276 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 30.93
SRR6202310 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 30.11
SRR6202355 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 29.88
SRR6202277 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 29.07
SRR6202337 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 27.50
SRR6202278 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 26.52
SRR6202342 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00
SRR6202353 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00

Source: CnidoSite RNA-seq expression matrices (EDIAP_TPM, StringTie quantification over 72 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 Exaiptasia diaphana 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 correlated15KXJ20762.10.809040695488688
Negatively correlated6KXJ14838.1-0.687408960901882

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 Exaiptasia diaphana, 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
ChIP-seqH3K27ac_symbiont3Exon 1 · Promoter (1-2kb) 1 · Promoter (<=1kb) 1
H3K9ac_symbiont2Exon 1 · Promoter (<=1kb) 1
ATAC-seqMild_Stress_Aposym2Exon 1 · Promoter (1-2kb) 1

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

SampleMethylation profile
whole_animal_aposymbiotic_1open
whole_animal_aposymbiotic_2open
whole_animal_aposymbiotic_3open
whole_animal_aposymbiotic_4open
whole_animal_aposymbiotic_5open
whole_animal_aposymbiotic_6open
whole_animal_aposymbiotic_7open
whole_animal_aposymbiotic_8open
whole_animal_aposymbiotic_9open
whole_animal_symbiotic_1open
whole_animal_symbiotic_10open
whole_animal_symbiotic_11open
whole_animal_symbiotic_12open
whole_animal_symbiotic_13open
whole_animal_symbiotic_14open
whole_animal_symbiotic_2open
whole_animal_symbiotic_3open
whole_animal_symbiotic_4open
whole_animal_symbiotic_5open
whole_animal_symbiotic_6open
whole_animal_symbiotic_7open
whole_animal_symbiotic_8open
whole_animal_symbiotic_9open

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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