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Aliases for LDLRAD4 Gene

Aliases for LDLRAD4 Gene

  • Low Density Lipoprotein Receptor Class A Domain Containing 4 2 3 5
  • Clone 22 2 3
  • C18orf1 3 4
  • Low-Density Lipoprotein Receptor Class A Domain-Containing Protein 4 3
  • Chromosome 18 Open Reading Frame 1 2

External Ids for LDLRAD4 Gene

Previous HGNC Symbols for LDLRAD4 Gene

  • C18orf1

Summaries for LDLRAD4 Gene

GeneCards Summary for LDLRAD4 Gene

LDLRAD4 (Low Density Lipoprotein Receptor Class A Domain Containing 4) is a Protein Coding gene. GO annotations related to this gene include R-SMAD binding. An important paralog of this gene is PMEPA1.

UniProtKB/Swiss-Prot for LDLRAD4 Gene

  • Functions as a negative regulator of TGF-beta signaling and thereby probably plays a role in cell proliferation, differentiation, apoptosis, motility, extracellular matrix production and immunosuppression. In the canonical TGF-beta pathway, ZFYVE9/SARA recruits the intracellular signal transducer and transcriptional modulators SMAD2 and SMAD3 to the TGF-beta receptor. Phosphorylated by the receptor, SMAD2 and SMAD3 then form a heteromeric complex with SMAD4 that translocates to the nucleus to regulate transcription. Through interaction with SMAD2 and SMAD3, LDLRAD4 may compete with ZFYVE9 and SMAD4 and prevent propagation of the intracellular signal.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LDLRAD4 Gene

Genomics for LDLRAD4 Gene

Regulatory Elements for LDLRAD4 Gene

Enhancers for LDLRAD4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18F013538 1.6 FANTOM5 Ensembl ENCODE 16.6 +323.9 323888 6.0 MLX ZFP64 ARID4B DMAP1 ZNF48 YY1 SP5 MIER2 PPARG KAT8 LDLRAD4 RNMT LOC102724615 ENSG00000272746
GH18F013562 1.3 FANTOM5 ENCODE 15.9 +345.8 345789 2.5 HDGF TBP PKNOX1 TBL1XR1 WRNIP1 BMI1 EGR1 ETV6 RCOR1 CREM LDLRAD4 PSMG2 FAM210A RNMT ENSG00000267503 PIR42063
GH18F013450 1.2 FANTOM5 Ensembl ENCODE 15.9 +234.3 234303 2.8 ZNF263 ZNF664 JUND GLIS2 FOS ZIC2 MAFK LDLRAD4 GC18P013454 LDLRAD4-AS1
GH18F013610 1.3 FANTOM5 ENCODE 14 +396.3 396256 6.6 HDGF TBP PKNOX1 TBL1XR1 WRNIP1 SIN3A BMI1 RFX5 EGR1 SCRT2 LDLRAD4 RNMT FAM210A MIR4526 ENSG00000266954
GH18F013379 1.1 FANTOM5 ENCODE 14.5 +164.2 164239 4.0 MAX REST MNT ZIC2 RAD21 NR2F2 ZNF121 EED ETV6 FOXP2 LDLRAD4 RNMT PTPN2 CEP192 ENSG00000267393 LDLRAD4-AS1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LDLRAD4 on UCSC Golden Path with GeneCards custom track

Promoters for LDLRAD4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001811648 802 2601 ZNF76 RAD21 ZNF48 ZNF335 GLIS2 SP3 ZEB2 GLIS1 MXD3 ZBTB26

Genomic Location for LDLRAD4 Gene

Chromosome:
18
Start:
13,217,498 bp from pter
End:
13,652,755 bp from pter
Size:
435,258 bases
Orientation:
Plus strand

Genomic View for LDLRAD4 Gene

Genes around LDLRAD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LDLRAD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LDLRAD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LDLRAD4 Gene

Proteins for LDLRAD4 Gene

  • Protein details for LDLRAD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15165-LRAD4_HUMAN
    Recommended name:
    Low-density lipoprotein receptor class A domain-containing protein 4
    Protein Accession:
    O15165
    Secondary Accessions:
    • B3KNT9
    • E9PAY9
    • K7EN38
    • O15166
    • O15167
    • O15168
    • Q5U646
    • Q6NXP3

    Protein attributes for LDLRAD4 Gene

    Size:
    306 amino acids
    Molecular mass:
    33900 Da
    Quaternary structure:
    • Interacts with PMEPA1. Interacts (via the SMAD interaction motif) with SMAD2 and SMAD3.

    Alternative splice isoforms for LDLRAD4 Gene

neXtProt entry for LDLRAD4 Gene

Post-translational modifications for LDLRAD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LDLRAD4 Gene

Domains & Families for LDLRAD4 Gene

Protein Domains for LDLRAD4 Gene

Suggested Antigen Peptide Sequences for LDLRAD4 Gene

Graphical View of Domain Structure for InterPro Entry

O15165

UniProtKB/Swiss-Prot:

LRAD4_HUMAN :
  • The SMAD interaction motif is required for interaction with SMAD2 and SMAD3 and the negative regulation of TGF-beta signaling.
  • Belongs to the PMEPA1 family.
Domain:
  • The SMAD interaction motif is required for interaction with SMAD2 and SMAD3 and the negative regulation of TGF-beta signaling.
  • Contains 1 LDL-receptor class A domain.
Family:
  • Belongs to the PMEPA1 family.
genes like me logo Genes that share domains with LDLRAD4: view

No data available for Gene Families for LDLRAD4 Gene

Function for LDLRAD4 Gene

Molecular function for LDLRAD4 Gene

UniProtKB/Swiss-Prot Function:
Functions as a negative regulator of TGF-beta signaling and thereby probably plays a role in cell proliferation, differentiation, apoptosis, motility, extracellular matrix production and immunosuppression. In the canonical TGF-beta pathway, ZFYVE9/SARA recruits the intracellular signal transducer and transcriptional modulators SMAD2 and SMAD3 to the TGF-beta receptor. Phosphorylated by the receptor, SMAD2 and SMAD3 then form a heteromeric complex with SMAD4 that translocates to the nucleus to regulate transcription. Through interaction with SMAD2 and SMAD3, LDLRAD4 may compete with ZFYVE9 and SMAD4 and prevent propagation of the intracellular signal.

Gene Ontology (GO) - Molecular Function for LDLRAD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070412 R-SMAD binding IPI 24627487
genes like me logo Genes that share ontologies with LDLRAD4: view
genes like me logo Genes that share phenotypes with LDLRAD4: view

Animal Models for LDLRAD4 Gene

MGI Knock Outs for LDLRAD4:

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LDLRAD4 Gene

Localization for LDLRAD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LDLRAD4 Gene

Early endosome membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LDLRAD4 gene
Compartment Confidence
nucleus 5
endosome 5
plasma membrane 3
extracellular 2
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for LDLRAD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 9479497
GO:0031901 early endosome membrane IEA --
genes like me logo Genes that share ontologies with LDLRAD4: view

Pathways & Interactions for LDLRAD4 Gene

SuperPathways for LDLRAD4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LDLRAD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009968 negative regulation of signal transduction IEA --
GO:0010719 negative regulation of epithelial to mesenchymal transition IMP 24627487
GO:0010991 negative regulation of SMAD protein complex assembly IDA 24627487
GO:0030336 negative regulation of cell migration IMP 24627487
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway IMP 24627487
genes like me logo Genes that share ontologies with LDLRAD4: view

No data available for Pathways by source and SIGNOR curated interactions for LDLRAD4 Gene

Transcripts for LDLRAD4 Gene

Unigene Clusters for LDLRAD4 Gene

Low density lipoprotein receptor class A domain containing 4:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LDLRAD4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c · 11d · 11e
SP1: - - - - - -
SP2: - - - - -
SP3: - -
SP4: -
SP5: - -
SP6:
SP7: - -
SP8:
SP9: -

Relevant External Links for LDLRAD4 Gene

GeneLoc Exon Structure for
LDLRAD4
ECgene alternative splicing isoforms for
LDLRAD4

Expression for LDLRAD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LDLRAD4 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LDLRAD4 Gene



NURSA nuclear receptor signaling pathways regulating expression of LDLRAD4 Gene:

LDLRAD4

SOURCE GeneReport for Unigene cluster for LDLRAD4 Gene:

Hs.731853

mRNA Expression by UniProt/SwissProt for LDLRAD4 Gene:

O15165-LRAD4_HUMAN
Tissue specificity: Expressed in lymphocytes.
genes like me logo Genes that share expression patterns with LDLRAD4: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Protein tissue co-expression partners for LDLRAD4 Gene

Orthologs for LDLRAD4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LDLRAD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LDLRAD4 34 35
  • 99.46 (n)
oppossum
(Monodelphis domestica)
Mammalia LDLRAD4 35
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ldlrad4 34
  • 88.56 (n)
mouse
(Mus musculus)
Mammalia Ldlrad4 34 16 35
  • 88.45 (n)
dog
(Canis familiaris)
Mammalia LDLRAD4 34 35
  • 83.22 (n)
cow
(Bos Taurus)
Mammalia LDLRAD4 34 35
  • 82.18 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LDLRAD4 35
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves LDLRAD4 35
  • 85 (a)
OneToOne
C2H18ORF1 34
  • 80.87 (n)
lizard
(Anolis carolinensis)
Reptilia LDLRAD4 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ldlrad4 34
  • 77.67 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC556780 34
  • 70.33 (n)
ldlrad4 35
  • 65 (a)
OneToMany
LDLRAD4 (2 of 2) 35
  • 61 (a)
OneToMany
Species where no ortholog for LDLRAD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LDLRAD4 Gene

ENSEMBL:
Gene Tree for LDLRAD4 (if available)
TreeFam:
Gene Tree for LDLRAD4 (if available)

Paralogs for LDLRAD4 Gene

Paralogs for LDLRAD4 Gene

(2) SIMAP similar genes for LDLRAD4 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LDLRAD4: view

Variants for LDLRAD4 Gene

Sequence variations from dbSNP and Humsavar for LDLRAD4 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs1006083 -- 13,441,747(+) CACAG(A/G)AGCTC intron-variant, nc-transcript-variant
rs1007922 -- 13,438,544(-) CATGC(C/T)GTCCC intron-variant, nc-transcript-variant
rs10083911 -- 13,357,438(+) tattt(A/G)ttaaa intron-variant
rs10084046 -- 13,330,369(+) tcata(A/G)tacat intron-variant
rs10163688 -- 13,316,257(+) gaaag(G/T)acagc intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LDLRAD4 Gene

Variant ID Type Subtype PubMed ID
nsv833591 CNV gain 17160897
nsv828184 CNV gain 20364138
nsv828183 CNV gain 20364138
nsv576529 CNV gain 21841781
nsv576528 CNV gain 21841781
nsv475369 CNV novel sequence insertion 20440878
nsv2211 CNV insertion 18451855
nsv2209 CNV deletion 18451855
nsv131518 CNV deletion 16902084
nsv131306 CNV deletion 16902084
nsv1160507 CNV deletion 26073780
nsv1144828 CNV deletion 24896259
nsv1112299 CNV deletion 24896259
nsv1076812 CNV insertion 25765185
nsv1071432 CNV deletion 25765185
esv998847 CNV insertion 20482838
esv3641858 CNV loss 21293372
esv3641857 CNV loss 21293372
esv3641855 CNV loss 21293372
esv3555083 CNV deletion 23714750
esv3448583 CNV duplication 20981092
esv3405323 CNV duplication 20981092
esv28046 CNV loss 19812545
esv2716821 CNV deletion 23290073
esv2671365 CNV deletion 23128226
esv2662984 CNV deletion 23128226
esv2657044 CNV deletion 23128226
esv26175 CNV gain+loss 19812545
esv2182710 CNV deletion 18987734
esv1008130 CNV loss 20482838
dgv1853e59 CNV duplication 20981092

Variation tolerance for LDLRAD4 Gene

Residual Variation Intolerance Score: 29.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.39; 27.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LDLRAD4 Gene

Human Gene Mutation Database (HGMD)
LDLRAD4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LDLRAD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LDLRAD4 Gene

Disorders for LDLRAD4 Gene

Relevant External Links for LDLRAD4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LDLRAD4

No disorders were found for LDLRAD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LDLRAD4 Gene

Publications for LDLRAD4 Gene

  1. C18 ORF1, a novel negative regulator of transforming growth factor- beta signaling. (PMID: 24627487) Nakano N. … Itoh S. (J. Biol. Chem. 2014) 2 3 4 64
  2. Multiple transcriptional variants and RNA editing in C18orf1, a novel gene with LDLRA and transmembrane domains on 18p11.2. (PMID: 9479497) Yoshikawa T. … Detera-Wadleigh S.D. (Genomics 1998) 2 3 4 64
  3. Analysis of a t(18;21)(p11.1;p11.1) translocation in a family with schizophrenia. (PMID: 19461657) Meerabux J.M. … Yoshikawa T. (J. Hum. Genet. 2009) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LDLRAD4 Gene

Sources for LDLRAD4 Gene

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