Detailed information of FUN_011618-T1 in Colpophyllia natans

Genomic Location: contig_16:5359337...5392715
NR annotation: XP_020622762.1, uncharacterized protein LOC110060335 [Orbicella faveolata]
Species Colpophyllia natans · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q6V1P9Protocadherin-23 OS=Homo sapiens OX=9606 GN=DCHS2 PE=1 SV=2
Q2PZL6Protocadherin Fat 4 OS=Mus musculus OX=10090 GN=Fat4 PE=1 SV=2
P58365Cadherin-23 OS=Rattus norvegicus OX=10116 GN=Cdh23 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0010997 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00028
all species →
CadherinCadherin domainDomainInterproscan
PF13385
all species →
Laminin_G_3Concanavalin A-like lectin/glucanases superfamilyDomainInterproscan
PF00102
all species →
Y_phosphataseProtein-tyrosine phosphataseDomainInterproscan
PF00055
all species →
Laminin_NLaminin N-terminal (Domain VI)DomainInterproscan
PF16070
all species →
TMEM132Transmembrane protein family 132FamilyInterproscan
PF00041
all species →
fn3Fibronectin type III domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002126
all species →
DomainCadherin-likeInterproscan
IPR015919
all species →
Homologous_superfamilyCadherin-like superfamilyInterproscan
IPR003595
all species →
DomainProtein-tyrosine phosphatase, catalyticInterproscan
IPR036439
all species →
Homologous_superfamilyDockerin domain superfamilyInterproscan
IPR000387
all species →
DomainTyrosine-specific protein phosphatases domainInterproscan
IPR029021
all species →
Homologous_superfamilyProtein-tyrosine phosphatase-likeInterproscan
IPR000242
all species →
DomainTyrosine-specific protein phosphatase, PTPase domainInterproscan
IPR039808
all species →
FamilyCadherinInterproscan
IPR008965
all species →
Homologous_superfamilyCBM2/CBM3, carbohydrate-binding domain superfamilyInterproscan
IPR018247
all species →
Binding_siteEF-Hand 1, calcium-binding siteInterproscan
IPR003961
all species →
DomainFibronectin type IIIInterproscan
IPR020894
all species →
Conserved_siteCadherin conserved siteInterproscan
IPR008211
all species →
DomainLaminin, N-terminalInterproscan
IPR048287
all species →
DomainThrombospondin-like, N-terminal domainInterproscan
IPR036116
all species →
Homologous_superfamilyFibronectin type III superfamilyInterproscan
IPR031437
all species →
DomainTransmembrane protein family 132, middle domainInterproscan
IPR013320
all species →
Homologous_superfamilyConcanavalin A-like lectin/glucanase domain superfamilyInterproscan
IPR016130
all species →
Active_siteProtein-tyrosine phosphatase, active siteInterproscan
IPR013783
all species →
Homologous_superfamilyImmunoglobulin-like foldInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24027
all species →
CADHERIN-23Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005509
all species →
Molecular Functioncalcium ion bindingInterproscan
GO:0007156
all species →
Biological Processhomophilic cell adhesion via plasma membrane adhesion moleculesInterproscan
GO:0016020
all species →
Cellular ComponentmembraneInterproscan
GO:0000272
all species →
Biological Processpolysaccharide catabolic processInterproscan
GO:0016311
all species →
Biological ProcessdephosphorylationInterproscan
GO:0004725
all species →
Molecular Functionprotein tyrosine phosphatase activityInterproscan
GO:0006470
all species →
Biological Processprotein dephosphorylationInterproscan
GO:0016342
all species →
Cellular Componentcatenin complexInterproscan
GO:0045296
all species →
Molecular Functioncadherin bindingInterproscan
GO:0098609
all species →
Biological Processcell-cell adhesionInterproscan
GO:0098742
all species →
Biological Processcell-cell adhesion via plasma-membrane adhesion moleculesInterproscan
GO:0030246
all species →
Molecular Functioncarbohydrate bindingInterproscan
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0005886
all species →
Cellular Componentplasma membraneInterproscan
GO:0007155
all species →
Biological Processcell adhesionInterproscan

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
No KEGG orthology assignment for FUN_011618-T1.

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 Colpophyllia natans 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 Colpophyllia natans, 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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