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Aliases for SCARF1 Gene

Aliases for SCARF1 Gene

  • Scavenger Receptor Class F Member 1 2 3 5
  • Acetyl LDL Receptor 2 3 4
  • Scavenger Receptor Expressed By Endothelial Cells 1 3 4
  • SREC-I 3 4
  • SREC 3 4
  • Scavenger Receptor Expressed By Endothelial Cells 2
  • Scavenger Receptor Class F, Member 1 2
  • KIAA0149 4
  • SREC1 3

External Ids for SCARF1 Gene

Previous GeneCards Identifiers for SCARF1 Gene

  • GC17P001630
  • GC17M001872
  • GC17M001487
  • GC17M001743
  • GC17M001484
  • GC17M001485
  • GC17M001537
  • GC17M001436

Summaries for SCARF1 Gene

Entrez Gene Summary for SCARF1 Gene

  • The protein encoded by this gene is a scavenger receptor that is expressed in endothelial cells. It regulates the uptake of chemically modified low density lipoproteins, including acetylated low density lipoprotein (Ac-LDL), and it may be involved in atherogenesis. This gene is regulated by the transcription factors ZNF444/EZF-2 and SP1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

GeneCards Summary for SCARF1 Gene

SCARF1 (Scavenger Receptor Class F Member 1) is a Protein Coding gene. Diseases associated with SCARF1 include Syndromic X-Linked Intellectual Disability Snyder Type and Urethral Stricture. Among its related pathways are Binding and Uptake of Ligands by Scavenger Receptors and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include transmembrane signaling receptor activity and low-density lipoprotein particle binding. An important paralog of this gene is SCARF2.

UniProtKB/Swiss-Prot for SCARF1 Gene

  • Mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). Mediates heterophilic interactions, suggesting a function as adhesion protein. Plays a role in the regulation of neurite-like outgrowth (By similarity).

Additional gene information for SCARF1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCARF1 Gene

Genomics for SCARF1 Gene

GeneHancer (GH) Regulatory Elements for SCARF1 Gene

Promoters and enhancers for SCARF1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I001642 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 550.8 +1.1 1120 3.8 HDGF SIN3A BATF IRF4 ZNF121 GLIS2 ZNF207 ZNF143 ATF7 ETV6 SCARF1 RILP SLC43A2 GC17M001550
GH17I001648 Enhancer 0.9 ENCODE dbSUPER 550.8 -1.7 -1703 0.1 KLF1 PKNOX1 ZNF189 REST ZEB2 ZBTB8A ZIC2 HIC1 ZNF121 ZFHX2 SCARF1 RILP GC17M001550
GH17I001624 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.6 +18.3 18312 6.1 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 ZNF2 ZBTB7B ZNF213 ZNF207 SLC43A2 PITPNA ENSG00000263050 SMG6 HNRNPA1P16 ENSG00000263345 SCARF1 METTL16 MNT GLOD4
GH17I001604 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.1 +38.9 38856 5.2 HDGF PKNOX1 FOXA2 MLX IRF4 ZNF143 ATF7 RUNX3 SP5 JUNB SLC43A2 PITPNA SCARF1 WDR81 CRK GC17P001609 RN7SL105P GC17M001550
GH17I001616 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.8 +27.6 27615 3 HDGF HDAC1 PKNOX1 SMAD1 ATF1 INSM2 KLF17 RAD21 TCF12 ZNF121 PITPNA SLC43A2 SCARF1 WDR81 CRK HIC1 GC17P001609 GC17M001550
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCARF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARF1 gene promoter:

Genomic Locations for SCARF1 Gene

Genomic Locations for SCARF1 Gene
chr17:1,633,858-1,645,789
(GRCh38/hg38)
Size:
11,932 bases
Orientation:
Minus strand
chr17:1,537,152-1,549,041
(GRCh37/hg19)

Genomic View for SCARF1 Gene

Genes around SCARF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARF1 Gene

Proteins for SCARF1 Gene

  • Protein details for SCARF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14162-SREC_HUMAN
    Recommended name:
    Scavenger receptor class F member 1
    Protein Accession:
    Q14162
    Secondary Accessions:
    • A8MQ05
    • O43701
    • Q8NHD2
    • Q8NHD3
    • Q8NHD4
    • Q8NHD5

    Protein attributes for SCARF1 Gene

    Size:
    830 amino acids
    Molecular mass:
    87387 Da
    Quaternary structure:
    • Heterophilic interaction with SREC2 via its extracellular domain. The heterophilic interaction is suppressed by the presence of ligand such as Ac-LDL. Interacts with AVIL (By similarity).

    Alternative splice isoforms for SCARF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCARF1 Gene

Post-translational modifications for SCARF1 Gene

  • Glycosylation at isoforms=2, 3, 4, 5289, isoforms=3382, and isoforms=3393
  • Modification sites at PhosphoSitePlus

Other Protein References for SCARF1 Gene

No data available for DME Specific Peptides for SCARF1 Gene

Domains & Families for SCARF1 Gene

Gene Families for SCARF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for SCARF1 Gene

Suggested Antigen Peptide Sequences for SCARF1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCARF1: view

No data available for UniProtKB/Swiss-Prot for SCARF1 Gene

Function for SCARF1 Gene

Molecular function for SCARF1 Gene

UniProtKB/Swiss-Prot Function:
Mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). Mediates heterophilic interactions, suggesting a function as adhesion protein. Plays a role in the regulation of neurite-like outgrowth (By similarity).

Phenotypes From GWAS Catalog for SCARF1 Gene

Gene Ontology (GO) - Molecular Function for SCARF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity TAS 9395444
GO:0005044 scavenger receptor activity IDA,IEA 9395444
GO:0030169 low-density lipoprotein particle binding IDA 9395444
genes like me logo Genes that share ontologies with SCARF1: view
genes like me logo Genes that share phenotypes with SCARF1: view

Animal Models for SCARF1 Gene

MGI Knock Outs for SCARF1:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCARF1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCARF1 Gene

Localization for SCARF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCARF1 Gene

Membrane; Single-pass type I 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 SCARF1 gene
Compartment Confidence
plasma membrane 5
extracellular 3
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
endosome 1

Gene Ontology (GO) - Cellular Components for SCARF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IDA,IEA 9395444
GO:0030666 endocytic vesicle membrane TAS --
genes like me logo Genes that share ontologies with SCARF1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCARF1 Gene

Pathways & Interactions for SCARF1 Gene

genes like me logo Genes that share pathways with SCARF1: view

Pathways by source for SCARF1 Gene

Gene Ontology (GO) - Biological Process for SCARF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006707 cholesterol catabolic process IC 9395444
GO:0006898 receptor-mediated endocytosis IEA,TAS 9395444
GO:0007155 cell adhesion IEA --
GO:0007165 signal transduction IEA --
GO:0010976 positive regulation of neuron projection development ISS --
genes like me logo Genes that share ontologies with SCARF1: view

No data available for SIGNOR curated interactions for SCARF1 Gene

Drugs & Compounds for SCARF1 Gene

(1) Drugs for SCARF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for SCARF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SCARF1: view

Transcripts for SCARF1 Gene

Unigene Clusters for SCARF1 Gene

Scavenger receptor class F, member 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARF1 Gene

No ASD Table

Relevant External Links for SCARF1 Gene

GeneLoc Exon Structure for
SCARF1
ECgene alternative splicing isoforms for
SCARF1

Expression for SCARF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCARF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCARF1 Gene

This gene is overexpressed in Spleen (x4.9).

Protein differential expression in normal tissues from HIPED for SCARF1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (28.3), Heart (24.7), and Platelet (15.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SCARF1 Gene



Protein tissue co-expression partners for SCARF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SCARF1 Gene:

SCARF1

SOURCE GeneReport for Unigene cluster for SCARF1 Gene:

Hs.647430

mRNA Expression by UniProt/SwissProt for SCARF1 Gene:

Q14162-SREC_HUMAN
Tissue specificity: Endothelial cells.

Evidence on tissue expression from TISSUES for SCARF1 Gene

  • Blood(4.4)
  • Heart(4.4)
  • Bone marrow(4.2)
  • Liver(4.2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with SCARF1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SCARF1 Gene

Orthologs for SCARF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCARF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCARF1 33 34
  • 91.74 (n)
dog
(Canis familiaris)
Mammalia SCARF1 33 34
  • 84.41 (n)
cow
(Bos Taurus)
Mammalia SCARF1 33 34
  • 83.84 (n)
mouse
(Mus musculus)
Mammalia Scarf1 33 16 34
  • 78.08 (n)
rat
(Rattus norvegicus)
Mammalia Scarf1 33
  • 77.82 (n)
oppossum
(Monodelphis domestica)
Mammalia SCARF1 34
  • 59 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCARF1 34
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCARF1 33 34
  • 62.28 (n)
lizard
(Anolis carolinensis)
Reptilia SCARF1 34
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scarf1 33
  • 56.02 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100005273 33
  • 54.28 (n)
scarf1 34
  • 40 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta nimA 34
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 20 (a)
OneToMany
Species where no ortholog for SCARF1 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)
  • 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 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 SCARF1 Gene

ENSEMBL:
Gene Tree for SCARF1 (if available)
TreeFam:
Gene Tree for SCARF1 (if available)

Paralogs for SCARF1 Gene

Paralogs for SCARF1 Gene

(2) SIMAP similar genes for SCARF1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SCARF1: view

Variants for SCARF1 Gene

Sequence variations from dbSNP and Humsavar for SCARF1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000198744 -- 1,643,779(-) G/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000464998 -- 1,647,198(-) G/A upstream_transcript_variant
rs1000571232 -- 1,642,499(-) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001023622 -- 1,641,725(-) A/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001289560 -- 1,647,276(-) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SCARF1 Gene

Variant ID Type Subtype PubMed ID
nsv1059565 CNV gain 25217958
nsv457635 CNV gain 19166990
nsv516055 CNV gain+loss 19592680
nsv527897 CNV loss 19592680
nsv574211 CNV gain 21841781
nsv827855 CNV loss 20364138
nsv952100 CNV deletion 24416366

Variation tolerance for SCARF1 Gene

Residual Variation Intolerance Score: 97.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.83; 83.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCARF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCARF1 Gene

Disorders for SCARF1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SCARF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
syndromic x-linked intellectual disability snyder type
  • mental retardation, x-linked, snyder-robinson type
urethral stricture
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCARF1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCARF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCARF1 Gene

Publications for SCARF1 Gene

  1. Expression cloning of a novel scavenger receptor from human endothelial cells. (PMID: 9395444) Adachi H … Inoue K (The Journal of biological chemistry 1997) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 8590280) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1995) 2 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Characterization of the human gene encoding the scavenger receptor expressed by endothelial cell and its regulation by a novel transcription factor, endothelial zinc finger protein-2. (PMID: 11978792) Adachi H … Tsujimoto M (The Journal of biological chemistry 2002) 3 4 58
  5. Scavenger receptor SREC-I promotes double stranded RNA-mediated TLR3 activation in human monocytes. (PMID: 25641411) Murshid A … Calderwood SK (Immunobiology 2015) 3 58

Products for SCARF1 Gene

Sources for SCARF1 Gene

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