Gene detail

Detailed information of BRAKERYMEP00000009772.1 in Astreopora myriophthalma

Genomic Location: BLFK01000284.1:688547...701568
NR annotation: XP_044183207.1, low-density lipoprotein receptor-related protein 2-like [Acropora millepora]
Species Astreopora myriophthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERYMET00000009772

ATGATTTCAGTTGTGCTGATGGAAAGACTTGTATTGACAAGAAATGGGTTTGTGATAGAGATAATGACTGTGGAGACATGTCAGATGAAGTTGATTGCCCCACTGGTGAACCTTGTCAAAATGACCAGTTTGCATGTGGAAATGGTCATTGCATATTCCAGAGATGGGTTTGTGATCAAGAAAATGACTGTTCCGACTGGACTGATGAACTTAATTGCAGTGACAACGAGGCAGTGTGATGCAGCTACTGAGTTCAGATGCTCTGATGGAACATGCATAAATATCAACTGGAAATGCGATGGGGACGCTGACTGTGCTAACAAATCTGATGAACAAGGCTGTGGTCCTGTCACATGTTTACCCAACCAGTGGCAGTGTATTGGGACCACGCAGTGCTTGGCAATGGATCAAGTTTGCGATGGGAATAATGACTGTGGTGATAACTCAGATGAAGGGACACATTGCTATATAAATGAATGTTTAACGATCGGAATCTGTGATCATCATTGTGTTAACACCAATGGATCTTACAAGTGCTTTTGTGCGGAGGGCTATGTATTTGAGCCCCCACGGACGTGCCGACCTCAAGgaGTTAAAGAGCCATGGCTATTATTAGCAAACAGAAAGAGCATACGCCAAGCAAGCCTGGATGGTAATGTTTACAGTGACGTGTTCTCGAACTTGAGTCGTACAGTGGCTCTTGACTTTGATATCAGTGAAGGCAAACTGTACTGGACGGATGTGATCAACAATGCCATATATAGTACACGCATTGTGTTAGATAAGTACGGCAGCCATCCTGGGAAGGTGCAAGCAATTGTAAAAGATGGACTAGCCGTACCAGTTGGCATTGCCGTTGACTGGGTGgccaaaaatttgtattttgtggaTAGCTCTGCCAGGCGGATCTTTGTTTGCAAACTGAATGGAAGCTACCTGTCATCGCTAATCACAAAAGATCTCGAAAATCCCAGGAGTATTGCGGTTGACCCGAGGGATGGTTACTTGTTCTGGACAGATTGGGGAATGCACAAGATAGAGAGAGCAGGAATGGACGGGTCAAACAGAACAGTGATTGCAAGCACAGGCATTTATTGGCCCAATGCACTCACCTTGGACTACCCAACACGTAAAATATATTGGGCAGATGCCCATTTTGATTACATAGGAGGCATGAGCTATGATGGCGGGGAGAGGAGAAGGATTCTTGGTCACCCATTAGTGGCTCATCCATTTGCTATAACTGTTTTTAGAAATGATTTATACTTCTCCGATTGGACGCGACAAGCCGTTGTGAAAGTGGACAAGTTTATTGCTAATGAAAGCAAAATCCTTTTGGGCGGCCTTAGACAGCCCATGGATGTCCAAGTGTATCACAGTGCGAGGCAACCACACACCTTTAATCCTTGTAACGACAGTAGTAAATGTGGTTGTCAGCAACTGTGTCTCGTCACTCCTGCACCGACAGGAGGCTGTGTATGCAGATGTATGATACGTTACAAATTGGCTACAGATAAGAAATCCTGCATTCTGCAAGATACTTTCTTAATTTACGCACGGGGGACCGAAATCGTAGGCATGCCCATTGAGGCTAATGCCTCTGGGGACACAATCGCACCTCTGCTCGGGCTTGGGAATGCCATGGGTCTGGACTACGATGCAAAAGAACAAATGATTTACTTTTCCGATATTGTGCGAGACAACATAAGCAGGTTCAGTATTAATACTAGAAAAGTCGAAGTGCTGGTAAATTCGGTTAAAAACGTTGATGGTATAGCGGTGGATTGGCTTGGACGGAACTTATATTGGACCGATGCCGAAGCACACGAGGTGGCAGTTGCTAAGCTGAATGGATCGTTCAAGAAAGTCTTGTTCCGTGAAGGTGTTTCACGGCCTAGGGCTATAATTTTGCACCCAGTGGAAGGGAAAATGTATTGGAGTGACTGGAATTCTCCAGCAAAAATAGAAGTGGCCAACATGGATGGCACAGCTCGTGACGTTTTAGTTCAGGGAAAAGGCCTTTCCTGGCCTAATGGTCTTAGCATCGACTACCAAGCAAGGAAGCTCTATTGGGCGGATGCATTGACAGACTTGATAGAATGTGCTGAGCTTGATGGTAGCAATCGCACTGCGATAGTGCGAGGTCTGTCACATCCATTTGGTCTTGATGTTGACAATGGCTTTGTCTATTGGACAGACTGGAGTAGCGAAGACATTCAGCGGGCAAGCATTAGCGATCCCTCGTCTCTTGTAGTTCTGAGATCTGGACTGAAGCATCTAATGGAAGTCCGGGTGTATAATCCCAAAAAACAGACAGGTGTGTCCAGTACTCTTAATTAA

Transcript

BRAKERYMET00000009772

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
C0HL13	Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1
A2ARV4	Low-density lipoprotein receptor-related protein 2 OS=Mus musculus OX=10090 GN=Lrp2 PE=1 SV=1
P98158	Low-density lipoprotein receptor-related protein 2 OS=Rattus norvegicus OX=10116 GN=Lrp2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004729 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07645 all species →	EGF_CA	Calcium-binding EGF domain	Domain	Interproscan
PF00057 all species →	Ldl_recept_a	Low-density lipoprotein receptor domain class A	Repeat	Interproscan
PF00058 all species →	Ldl_recept_b	Low-density lipoprotein receptor repeat class B	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036055 all species →	Homologous_superfamily	LDL receptor-like superfamily	Interproscan
IPR002172 all species →	Repeat	Low-density lipoprotein (LDL) receptor class A repeat	Interproscan
IPR050778 all species →	Family	Cueball/EGF/LRP/Nidogen	Interproscan
IPR000033 all species →	Repeat	LDLR class B repeat	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR000152 all species →	PTM	EGF-type aspartate/asparagine hydroxylation site	Interproscan
IPR023415 all species →	Conserved_site	Low-density lipoprotein (LDL) receptor class A, conserved site	Interproscan
IPR011042 all species →	Homologous_superfamily	Six-bladed beta-propeller, TolB-like	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan
IPR049883 all species →	Domain	NOTCH1 EGF-like calcium-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46513 all species →	VITELLOGENIN RECEPTOR-LIKE PROTEIN-RELATED-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan

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 BRAKERYMEP00000009772.1.

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 Astreopora myriophthalma 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 Astreopora myriophthalma, 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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw 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 / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →