Detailed information of anas_s0017.g56.t1 in Acropora nasuta

Genomic Location: sc0000017_pilon:1010684...1033628
NR annotation: XP_029197633.2, LOW QUALITY PROTEIN: neurogenic locus notch homolog protein 1-like [Acropora millepora]
Species Acropora nasuta · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9QW30Neurogenic locus notch homolog protein 2 OS=Rattus norvegicus OX=10116 GN=Notch2 PE=1 SV=1
G3I6Z6Neurogenic locus notch homolog protein 1 OS=Cricetulus griseus OX=10029 GN=NOTCH1 PE=1 SV=2
Q07008Neurogenic locus notch homolog protein 1 OS=Rattus norvegicus OX=10116 GN=Notch1 PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003337 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF07645
all species →
EGF_CACalcium-binding EGF domainDomainInterproscan
PF12796
all species →
Ank_2Ankyrin repeats (3 copies)RepeatInterproscan
PF07684
all species →
NODPNOTCH proteinFamilyInterproscan
PF13857
all species →
Ank_5Ankyrin repeats (many copies)RepeatInterproscan
PF06816
all species →
NODNOTCH proteinFamilyInterproscan
PF12661
all species →
hEGFHuman growth factor-like EGFDomainInterproscan
PF00066
all species →
NotchLNR domainDomainInterproscan
PF00008
all species →
EGFEGF-like domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000742
all species →
DomainEGF-like domainInterproscan
IPR049883
all species →
DomainNOTCH1 EGF-like calcium-binding domainInterproscan
IPR000152
all species →
PTMEGF-type aspartate/asparagine hydroxylation siteInterproscan
IPR008297
all species →
FamilyNotchInterproscan
IPR050906
all species →
FamilyNotch signaling pathwayInterproscan
IPR009030
all species →
Homologous_superfamilyGrowth factor receptor cysteine-rich domain superfamilyInterproscan
IPR010660
all species →
DomainNotch, NOD domainInterproscan
IPR002110
all species →
RepeatAnkyrin repeatInterproscan
IPR018097
all species →
Conserved_siteEGF-like calcium-binding, conserved siteInterproscan
IPR011656
all species →
DomainNotch, NODP domainInterproscan
IPR035993
all species →
Homologous_superfamilyNotch-like domain superfamilyInterproscan
IPR036770
all species →
Homologous_superfamilyAnkyrin repeat-containing domain superfamilyInterproscan
IPR000800
all species →
DomainNotch domainInterproscan
IPR013032
all species →
Conserved_siteEGF-like, conserved siteInterproscan
IPR001881
all species →
DomainEGF-like calcium-binding domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24044
all species →
NOTCH LIGAND FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0007219
all species →
Biological ProcessNotch signaling pathwayInterproscan
GO:0016020
all species →
Cellular ComponentmembraneInterproscan
GO:0030154
all species →
Biological Processcell differentiationInterproscan
GO:0050793
all species →
Biological Processregulation of developmental processInterproscan
GO:0005112
all species →
Molecular FunctionNotch bindingInterproscan
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0005509
all species →
Molecular Functioncalcium ion bindingInterproscan
GO:0007275
all species →
Biological Processmulticellular organism developmentInterproscan

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
K02599NOTCH1; Notch 1-Endocrine resistanceko01522deepkoala

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 Acropora nasuta 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 Acropora nasuta, 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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