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

Summary

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: mouse all
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Genomic context

Location:: 17p13.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (1633858..1645732, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (1522663..1534522, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (1537152..1549026, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
The Role of SREC- in Innate Immunity to Aspergillus fumigatus Keratitis.
Title: The Role of SREC-Ⅰ in Innate Immunity to Aspergillus fumigatus Keratitis.
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.
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.
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.
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.
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.
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).
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

L18426 (e-PCR)
- UniSTS:34648

STS-T96691 (e-PCR)
- UniSTS:67937

D1S1423 (e-PCR)
- UniSTS:149619

D17S1533 (e-PCR)
- UniSTS:16532

RH41938 (e-PCR)
- UniSTS:89762

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)

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
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

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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

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

NT_187611.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

63886..75760 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

1522663..1534522 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.
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.