Detailed information of amic_s0162.g8.t2 in Acropora microphthalma

Genomic Location: sc0000162_pilon:230376...323745
NR annotation: XP_044183207.1, low-density lipoprotein receptor-related protein 2-like [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
A2ARV4Low-density lipoprotein receptor-related protein 2 OS=Mus musculus OX=10090 GN=Lrp2 PE=1 SV=1
P98158Low-density lipoprotein receptor-related protein 2 OS=Rattus norvegicus OX=10116 GN=Lrp2 PE=1 SV=1
C0HL13Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004729 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00058
all species →
Ldl_recept_bLow-density lipoprotein receptor repeat class BRepeatInterproscan
PF14670
all species →
FXa_inhibitionCoagulation Factor Xa inhibitory siteDomainInterproscan
PF07645
all species →
EGF_CACalcium-binding EGF domainDomainInterproscan
PF00057
all species →
Ldl_recept_aLow-density lipoprotein receptor domain class ARepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036055
all species →
Homologous_superfamilyLDL receptor-like superfamilyInterproscan
IPR002172
all species →
RepeatLow-density lipoprotein (LDL) receptor class A repeatInterproscan
IPR000033
all species →
RepeatLDLR class B repeatInterproscan
IPR023415
all species →
Conserved_siteLow-density lipoprotein (LDL) receptor class A, conserved siteInterproscan
IPR000742
all species →
DomainEGF-like domainInterproscan
IPR011042
all species →
Homologous_superfamilySix-bladed beta-propeller, TolB-likeInterproscan
IPR049883
all species →
DomainNOTCH1 EGF-like calcium-binding domainInterproscan
IPR000152
all species →
PTMEGF-type aspartate/asparagine hydroxylation siteInterproscan
IPR051221
all species →
FamilyLow-density lipoprotein receptor-relatedInterproscan
IPR001881
all species →
DomainEGF-like calcium-binding domainInterproscan
IPR018097
all species →
Conserved_siteEGF-like calcium-binding, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR22722
all species →
LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0005886
all species →
Cellular Componentplasma membraneInterproscan
GO:0006898
all species →
Biological Processreceptor-mediated endocytosisInterproscan
GO:0016324
all species →
Cellular Componentapical plasma membraneInterproscan
GO:0042562
all species →
Molecular Functionhormone bindingInterproscan
GO:0043235
all species →
Cellular Componentreceptor complexInterproscan
GO:0005509
all species →
Molecular Functioncalcium ion bindingInterproscan

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 amic_s0162.g8.t2.

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 microphthalma 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 microphthalma, 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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