Detailed information of BRAKERXEIP00000054078.1 in Muricea muricata

Genomic Location: chr9:12251675...12268277
NR annotation: CAB3990434.1, CCR4-NOT transcription complex subunit 3 [Paramuricea clavata]
Species Muricea muricata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q8K0V4CCR4-NOT transcription complex subunit 3 OS=Mus musculus OX=10090 GN=Cnot3 PE=1 SV=1
O75175CCR4-NOT transcription complex subunit 3 OS=Homo sapiens OX=9606 GN=CNOT3 PE=1 SV=1
O13870General negative regulator of transcription subunit 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=not3 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002999 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04153
all species →
NOT2_3_5_CNOT2/NOT3/NOT5 C-terminalDomainInterproscan
PF04065
all species →
Not3Not1 N-terminal domain, CCR4-Not complex component FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR007282
all species →
DomainNOT2/NOT3/NOT5, C-terminalInterproscan
IPR007207
all species →
DomainCCR4-Not complex component, Not N-terminal domainInterproscan
IPR038635
all species →
Homologous_superfamilyCCR4-NOT complex subunit 2/3/5, C-terminal domain superfamilyInterproscan
IPR012270
all species →
FamilyCCR4-NOT complex, subunit 3/ 5Interproscan
IPR040168
all species →
FamilyNot2/Not3/Not5Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23326
all species →
CCR4 NOT-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006355
all species →
Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0005634
all species →
Cellular ComponentnucleusInterproscan
GO:0030015
all species →
Cellular ComponentCCR4-NOT core complexInterproscan
GO:0000289
all species →
Biological Processnuclear-transcribed mRNA poly(A) tail shorteningInterproscan
GO:0000932
all species →
Cellular ComponentP-bodyInterproscan
GO:2000036
all species →
Biological Processregulation of stem cell population maintenanceInterproscan

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
K12580CNOT3, NOT3; CCR4-NOT transcription complex subunit 3-Messenger RNA biogenesisko03019deepkoala

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

Co-expression network

Genes whose expression across the transcriptome samples of Muricea muricata 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Muricea muricata, 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.no expression matrix
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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