Detailed information of gfas1.m1.22366.m1 in Galaxea fascicularis

Genomic Location: xfSc0003380:2017...2613
NR annotation: XP_015760454.1, PREDICTED: COMM domain-containing protein 4-like [Acropora digitifera]
Species Galaxea fascicularis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9CQ02COMM domain-containing protein 4 OS=Mus musculus OX=10090 GN=Commd4 PE=1 SV=1
Q9H0A8COMM domain-containing protein 4 OS=Homo sapiens OX=9606 GN=COMMD4 PE=1 SV=1
Q5E9V6COMM domain-containing protein 4 OS=Bos taurus OX=9913 GN=COMMD4 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0009286 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF21672
all species →		COMM_HNCOMMD protein HN domainDomainInterproscan
PF07258
all species →		COMM_domainCOMM domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR017920
all species →		DomainCOMM domainInterproscan
IPR047155
all species →		FamilyCOMM domain-containing protein 4/6/7/8Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR16231
all species →		COMM DOMAIN-CONTAINING PROTEIN 4-8 FAMILY MEMBERInterproscan

 Gene Ontology
No Gene Ontology signature was recorded for gfas1.m1.22366.m1 in Galaxea fascicularis.
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
K22560COMMD4; COMM domain containing 4-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 gfas1.m1.22366.m1 across 22 RNA-seq samples of Galaxea fascicularis. 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.

22Samples
18TPM > 0
4Conditions
131.7Max TPM
62.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral holosome · Control 7 6 65.47 118.10
coral holosome · 30ic treatment 6 4 38.81 75.55
coral holosome · Prometryn (herbicidess) treatment 5 4 79.45 131.74
coral holosome · Prometryn (herbicidess) and 30ic treatment 4 4 74.12 120.62

Per sample · hover a bar for the full sample record

Show the sample table (22 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR27118485 coral holosome · Control coral holosome not recorded Control SRP476288 118.10
SRR27118492 coral holosome · Control coral holosome not recorded Control SRP476288 103.27
SRR27118488 coral holosome · Control coral holosome not recorded Control SRP476288 88.84
SRR27118487 coral holosome · Control coral holosome not recorded Control SRP476288 73.03
SRR27118486 coral holosome · Control coral holosome not recorded Control SRP476288 41.39
SRR27118491 coral holosome · Control coral holosome not recorded Control SRP476288 33.65
SRR27118480 coral holosome · Control coral holosome not recorded Control SRP476288 0.00
SRR27118476 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 75.55
SRR27118479 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 64.52
SRR27118478 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 49.96
SRR27118466 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 42.83
SRR27118468 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 0.00
SRR27118477 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 0.00
SRR27118482 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 131.74
SRR27118483 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 107.07
SRR27118469 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 102.34
SRR27118481 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 56.10
SRR27118484 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 0.00
SRR27118489 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 120.62
SRR27118472 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 64.66
SRR27118490 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 61.17
SRR27118475 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 50.02

Source: CnidoSite RNA-seq expression matrices (GFASC_TPM, StringTie quantification over 22 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 Galaxea fascicularis 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 correlated10gfas1.m1.1178.m10.804354589389451
Negatively correlated44gfas1.m1.11120.m1-0.857974889550274

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 Galaxea fascicularis, 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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