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SCARF1 scavenger receptor class F member 1 [ Homo sapiens (human) ]

Gene ID: 8578, updated on 11-Apr-2024

Summary

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Official Symbol
SCARF1provided by HGNC
Official Full Name
scavenger receptor class F member 1provided by HGNC
Primary source
HGNC:HGNC:16820
See related
Ensembl:ENSG00000074660 MIM:607873; AllianceGenome:HGNC:16820
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SREC; SREC1; SREC-I
Summary
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]
Expression
Broad expression in spleen (RPKM 18.4), lung (RPKM 9.9) and 22 other tissues See more
Orthologs
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Genomic context

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See SCARF1 in Genome Data Viewer
Location:
17p13.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (1633858..1645732, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1522663..1534522, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1537152..1549026, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 43 member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1509837-1510602 Neighboring gene RNA, 7SL, cytoplasmic 105, pseudogene Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1530301-1530838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1530839-1531376 Neighboring gene Sharpr-MPRA regulatory region 224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1554397-1554907 Neighboring gene Rab interacting lysosomal protein Neighboring gene pre-mRNA processing factor 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The Role of SREC-Ⅰ in Innate Immunity to Aspergillus fumigatus Keratitis. Zhang R, et al. Invest Ophthalmol Vis Sci, 2021 Jul 1. PMID 34236384, Free PMC Article
  2. Molecular and Cellular Interactions of Scavenger Receptor SR-F1 With Complement C1q Provide Insights Into Its Role in the Clearance of Apoptotic Cells. Wicker-Planquart C, et al. Front Immunol, 2020. PMID 32296440, Free PMC Article
  3. SCARF-1 promotes adhesion of CD4(+) T cells to human hepatic sinusoidal endothelium under conditions of shear stress. Patten DA, et al. Sci Rep, 2017 Dec 14. PMID 29242513, Free PMC Article
  4. Hsp90-peptide complexes stimulate antigen presentation through the class II pathway after binding scavenger receptor SREC-I. Murshid A, et al. Immunobiology, 2014 Dec. PMID 25155057, Free PMC Article
  5. A nasal epithelial receptor for Staphylococcus aureus WTA governs adhesion to epithelial cells and modulates nasal colonization. Baur S, et al. PLoS Pathog, 2014 May. PMID 24788600, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SCARF1-Induced Efferocytosis Plays an Immunomodulatory Role in Humans, and Autoantibodies Targeting SCARF1 Are Produced in Patients with Systemic Lupus Erythematosus.
    Title: SCARF1-Induced Efferocytosis Plays an Immunomodulatory Role in Humans, and Autoantibodies Targeting SCARF1 Are Produced in Patients with Systemic Lupus Erythematosus.
  2. The Role of SREC- in Innate Immunity to Aspergillus fumigatus Keratitis.
    Title: The Role of SREC-Ⅰ in Innate Immunity to Aspergillus fumigatus Keratitis.
  3. Molecular and Cellular Interactions of Scavenger Receptor SR-F1 With Complement C1q Provide Insights Into Its Role in the Clearance of Apoptotic Cells.
    Title: Molecular and Cellular Interactions of Scavenger Receptor SR-F1 With Complement C1q Provide Insights Into Its Role in the Clearance of Apoptotic Cells.
  4. SCARF-1 promotes adhesion of CD4(+) T cells to human hepatic sinusoidal endothelium under conditions of shear stress
    Title: SCARF-1 promotes adhesion of CD4(+) T cells to human hepatic sinusoidal endothelium under conditions of shear stress.
  5. Scavenger receptor SREC-I promotes double stranded RNA-mediated TLR3 activation in human monocytes
    Title: Scavenger receptor SREC-I promotes double stranded RNA-mediated TLR3 activation in human monocytes.
  6. These studies in addition to our earlier findings showed SREC-I to play a primary role in chaperone-associated antigen uptake both through cross priming of MHC class I molecules and entry into the class II pathway.
    Title: Hsp90-peptide complexes stimulate antigen presentation through the class II pathway after binding scavenger receptor SREC-I.
  7. In several assay systems this type F-scavenger receptor, termed SREC-I, bound to cell wall techoic acid in a charge dependent manner and mediated adhesion to nasal epithelial cells in vitro.
    Title: A nasal epithelial receptor for Staphylococcus aureus WTA governs adhesion to epithelial cells and modulates nasal colonization.
  8. GP2 is a binding partner of the scavenger receptor expressed on endothelial cells I (SREC-I) but not of SR-AI and SR-BI. Dendritic cells express SREC-I and also bind and internalize GP2.
    Title: The zymogen granule protein 2 (GP2) binds to scavenger receptor expressed on endothelial cells I (SREC-I).
  9. SRECI binds to SRECII and has a similar tissue distribution pattern
    Title: SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain.
  10. Characterization of the gene and its regulation by a novel transcription factor, endothelial zinc protein-2
    Title: 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.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0149, MGC47738

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables low-density lipoprotein particle binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables low-density lipoprotein particle binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables scavenger receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables scavenger receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transmembrane signaling receptor activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cholesterol catabolic process IC
Inferred by Curator
more info
 PubMed 
involved_in dendrite development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron remodeling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of axon regeneration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of neuron projection development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in receptor-mediated endocytosis TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in endocytic vesicle membrane TAS
Traceable Author Statement
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
scavenger receptor class F member 1
Names
acetyl LDL receptor
scavenger receptor expressed by endothelial cells 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_003693.4 → NP_003684.2  scavenger receptor class F member 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_003684.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC130343, AK291810, CA434049
    Consensus CDS
    CCDS11007.1
    UniProtKB/Swiss-Prot
    A8MQ05, O43701, Q14162, Q8NHD2, Q8NHD3, Q8NHD4, Q8NHD5
    UniProtKB/TrEMBL
    A8K6Z5
    Related
    ENSP00000263071.4, ENST00000263071.9
    Conserved Domains (1) summary
    pfam16019
    Location:100 → 135
    CSRNP_N; Cysteine/serine-rich nuclear protein N-terminus

  2. NM_145350.3 → NP_663325.1  scavenger receptor class F member 1 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (3, also known as SREC-3) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AB052948, AC130343, CA434049
    Consensus CDS
    CCDS45564.1
    UniProtKB/Swiss-Prot
    Q14162
    Related
    ENSP00000458174.1, ENST00000571272.5
    Conserved Domains (1) summary
    pfam16019
    Location:100 → 135
    CSRNP_N; Cysteine/serine-rich nuclear protein N-terminus

RNA

  1. NR_028075.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB052947, AC130343, CA434049, DC429327
    Related
    ENST00000434376.6

  2. NR_102409.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5'-most exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC130343, AK310174, CA434049, DC429327

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    1633858..1645732 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187611.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    63886..75760 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1522663..1534522 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_145352.2: Suppressed sequence

    Description
    NM_145352.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NR_028076.1: Suppressed sequence

    Description
    NR_028076.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which retains an intron.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14162.3 GenPept UniProtKB/Swiss-Prot:Q14162

Gene LinkOut

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