Detailed information of g16883.t1 in Montipora capitata

Genomic Location: Sc0000728:80537...100915
NR annotation: XP_029198189.2, low-density lipoprotein receptor-related protein 4-like isoform X3 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P35951Low-density lipoprotein receptor OS=Mus musculus OX=10090 GN=Ldlr PE=1 SV=2
P35950Low-density lipoprotein receptor OS=Cricetulus griseus OX=10029 GN=LDLR PE=3 SV=2
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)OG0000259 (this species only) · gene tree & orthology

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

 InterPro
InterPro termTypeDescriptionSource
IPR000742
all species →		DomainEGF-like domainInterproscan
IPR000033
all species →		RepeatLDLR class B repeatInterproscan
IPR001881
all species →		DomainEGF-like calcium-binding domainInterproscan
IPR002172
all species →		RepeatLow-density lipoprotein (LDL) receptor class A repeatInterproscan
IPR049883
all species →		DomainNOTCH1 EGF-like calcium-binding domainInterproscan
IPR011042
all species →		Homologous_superfamilySix-bladed beta-propeller, TolB-likeInterproscan
IPR051221
all species →		FamilyLow-density lipoprotein receptor-relatedInterproscan
IPR036055
all species →		Homologous_superfamilyLDL receptor-like superfamilyInterproscan
IPR000152
all species →		PTMEGF-type aspartate/asparagine hydroxylation siteInterproscan
IPR023415
all species →		Conserved_siteLow-density lipoprotein (LDL) receptor class A, conserved siteInterproscan
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:0005509
all species →		Molecular Functioncalcium ion bindingInterproscan
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

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
K20053VLDLR; very low-density lipoprotein receptor-Membrane traffickingko04131deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g16883.t1 across 48 RNA-seq samples of Montipora capitata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

48Samples
46TPM > 0
3Conditions
124.4Max TPM
47.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 20 43.32 118.18
whole organisms · low pH treatment 15 15 51.42 124.43
whole organisms · extra low pH treatment pH treatment 12 11 47.92 109.15

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 118.18
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 110.51
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 103.02
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 84.41
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 80.48
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 80.01
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 41.28
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 40.83
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 40.83
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 39.20
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 32.46
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 30.31
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 29.40
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 24.49
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 22.65
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 8.46
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 7.27
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 5.63
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 5.25
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 5.08
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 0.00
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 124.43
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 113.58
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 100.63
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 86.82
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 84.04
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 83.96
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 36.60
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 29.94
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 29.24
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 23.52
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 22.80
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 21.08
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 5.51
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 5.15
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 4.06
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 109.15
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 107.41
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 95.86
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 74.57
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 40.46
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 38.16
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 38.03
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 35.22
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 26.43
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 6.91
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 2.83
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 0.00

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora capitata 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated42g8840.t10.976011970335329
Negatively correlated8g15190.t1-0.928857141586953

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora capitata, 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.readyopen →
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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