LOCUS       NM_182895               3463 bp    mRNA    linear   PRI 06-APR-2024
DEFINITION  Homo sapiens scavenger receptor class F member 2 (SCARF2),
            transcript variant 2, mRNA.
ACCESSION   NM_182895
VERSION     NM_182895.5
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3463)
  AUTHORS   Karaer,D. and Karaer,K.
  TITLE     Two novel variants in SCARF2 gene underlie van den Ende-Gupta
            syndrome
  JOURNAL   Am J Med Genet A 188 (6), 1881-1884 (2022)
   PUBMED   35224863
  REMARK    GeneRIF: Two novel variants in SCARF2 gene underlie van den
            Ende-Gupta syndrome.
REFERENCE   2  (bases 1 to 3463)
  AUTHORS   Hildebrandt,C.C., Patel,N., Graham,J.M. Jr., Bamshad,M.,
            Nickerson,D.A., White,J.J., Marvin,C.T., Miller,D.E., Grand,K.L.,
            Sanchez-Lara,P.A., Schweitzer,D., Al-Zaidan,H.I., Al Masseri,Z.,
            Alkuraya,F.S. and Lin,A.E.
  CONSRTM   University of Washington Center for Mendelian Genomics
  TITLE     Further delineation of van den Ende-Gupta syndrome: Genetic
            heterogeneity and overlap with congenital heart defects and
            skeletal malformations syndrome
  JOURNAL   Am J Med Genet A 185 (7), 2136-2149 (2021)
   PUBMED   33783941
  REMARK    GeneRIF: Further delineation of van den Ende-Gupta syndrome:
            Genetic heterogeneity and overlap with congenital heart defects and
            skeletal malformations syndrome.
REFERENCE   3  (bases 1 to 3463)
  AUTHORS   Migliavacca,M.P., Sobreira,N.L., Antonialli,G.P., Oliveira,M.M.,
            Melaragno,M.I., Casteels,I., de Ravel,T., Brunoni,D., Valle,D. and
            Perez,A.B.
  TITLE     Sclerocornea in a patient with van den Ende-Gupta syndrome
            homozygous for a SCARF2 microdeletion
  JOURNAL   Am J Med Genet A 164A (5), 1170-1174 (2014)
   PUBMED   24478002
  REMARK    GeneRIF: the full VDEGS phenotype may include sclerocornea
            resulting from homozygosity or compound heterozygosity for loss of
            function variants in SCARF2.
REFERENCE   4  (bases 1 to 3463)
  AUTHORS   Kuo,J.C., Han,X., Hsiao,C.T., Yates,J.R. 3rd and Waterman,C.M.
  TITLE     Analysis of the myosin-II-responsive focal adhesion proteome
            reveals a role for beta-Pix in negative regulation of focal
            adhesion maturation
  JOURNAL   Nat Cell Biol 13 (4), 383-393 (2011)
   PUBMED   21423176
REFERENCE   5  (bases 1 to 3463)
  AUTHORS   Anastasio,N., Ben-Omran,T., Teebi,A., Ha,K.C., Lalonde,E., Ali,R.,
            Almureikhi,M., Der Kaloustian,V.M., Liu,J., Rosenblatt,D.S.,
            Majewski,J. and Jerome-Majewska,L.A.
  TITLE     Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome
  JOURNAL   Am J Hum Genet 87 (4), 553-559 (2010)
   PUBMED   20887961
  REMARK    GeneRIF: Mutations in SCARF2 are responsible for Van Den Ende-Gupta
            syndrome.
REFERENCE   6  (bases 1 to 3463)
  AUTHORS   Bedeschi,M.F., Colombo,L., Mari,F., Hofmann,K., Rauch,A.,
            Gentilin,B., Renieri,A. and Clerici,D.
  TITLE     Unmasking of a Recessive SCARF2 Mutation by a 22q11.12 de novo
            Deletion in a Patient with Van den Ende-Gupta Syndrome
  JOURNAL   Mol Syndromol 1 (5), 239-245 (2010)
   PUBMED   22140376
REFERENCE   7  (bases 1 to 3463)
  AUTHORS   Wu,C., Ma,M.H., Brown,K.R., Geisler,M., Li,L., Tzeng,E., Jia,C.Y.,
            Jurisica,I. and Li,S.S.
  TITLE     Systematic identification of SH3 domain-mediated human
            protein-protein interactions by peptide array target screening
  JOURNAL   Proteomics 7 (11), 1775-1785 (2007)
   PUBMED   17474147
REFERENCE   8  (bases 1 to 3463)
  AUTHORS   Ishii,J., Adachi,H., Aoki,J., Koizumi,H., Tomita,S., Suzuki,T.,
            Tsujimoto,M., Inoue,K. and Arai,H.
  TITLE     SREC-II, a new member of the scavenger receptor type F family,
            trans-interacts with SREC-I through its extracellular domain
  JOURNAL   J Biol Chem 277 (42), 39696-39702 (2002)
   PUBMED   12154095
  REMARK    GeneRIF: SRECII binds to SRECI and has a similar tissue
            distribution pattern
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AB024433.1 and BC009326.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_182895.4.
            
            Summary: The protein encoded by this gene is similar to
            SCARF1/SREC-I, a scavenger receptor protein that mediates the
            binding and degradation of acetylated low density lipoprotein
            (Ac-LDL). This protein has only little activity of internalizing
            modified low density lipoproteins (LDL), but it can interact with
            SCARF1 through its extracellular domain. The association of this
            protein with SCARF1 is suppressed by the presence of scavenger
            ligands. Alternatively spliced transcript variants encoding
            distinct isoforms have been reported. [provided by RefSeq, Jul
            2008].
            
            Transcript Variant: This variant (2) lacks an in-frame segment
            within the coding region, as compared to variant 1. The resulting
            isoform (2) lacks an internal region, as compared to isoform 1.
            
            CCDS Note: This CCDS representation has been updated to correct a
            frameshifted segment in the 3' coding region, supported by
            transcript and orthologous alignments, and by the update of the
            GRCh37 reference genome assembly to the GRCh38 assembly.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB024433.1, AB052951.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000622235.5/ ENSP00000477564.2
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-3333              AB024433.1         1-3333
            3334-3463           BC009326.2         2451-2580
FEATURES             Location/Qualifiers
     source          1..3463
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="22"
                     /map="22q11.21"
     gene            1..3463
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /note="scavenger receptor class F member 2"
                     /db_xref="GeneID:91179"
                     /db_xref="HGNC:HGNC:19869"
                     /db_xref="MIM:613619"
     exon            1..244
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     CDS             72..2672
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; scavenger receptor expressed by endothelial
                     cells 2 protein"
                     /codon_start=1
                     /product="scavenger receptor class F member 2 isoform 2
                     precursor"
                     /protein_id="NP_878315.2"
                     /db_xref="CCDS:CCDS46666.1"
                     /db_xref="GeneID:91179"
                     /db_xref="HGNC:HGNC:19869"
                     /db_xref="MIM:613619"
                     /translation="MEGAGPRGAGPARRRGAGGPPSPLLPSLLLLLLLWMLPDTVAPQ
                     ELNPRGRNVCRAPGSQVPTCCAGWRQQGDECGIAVCEGNSTCSENEVCVRPGECRCRH
                     GYFGANCDTKCPRQFWGPDCKELCSCHPHGQCEDVTGQCTCHARRWGARCEHACQCQH
                     GTCHPRSGACRCEPGWWGAQCASACYCSATSRCDPQTGACLCHAGWWGRSCNNQCACN
                     SSPCEQQSGRCQCRERTFGARCDRYCQCFRGRCHPVDGTCACEPGYRGKYCREPCPAG
                     FYGLGCRRRCGQCKGQQPCTVAEGRCLTCEPGWNGTKCDQPCATGFYGEGCSHRCPPC
                     RDGHACNHVTGKCTRCNAGWIGDRCETKCSNGTYGEDCAFVCADCGSGHCDFQSGRCL
                     CSPGVHGPHCNVTCPPGLHGADCAQACSCHEDTCDPVTGACHLETNQRKGVMGAGALL
                     VLLVCLLLSLLGCCCACRGKDPTRRELSLGRKKAPHRLCGRFSRISMKLPRIPLRRQK
                     LPKVVVAHHDLDNTLNCSFLEPPSGLEQPSPSWSSRASFSSFDTTDEGPVYCVPHEEA
                     PAESRDPEVPTVPAEAPAPSPVPLTTPASAEEAIPLPASSDSERSASSVEGPGGALYA
                     RVARREARPARARGEIGGLSLSPSPERRKPPPPDPATKPKVSWIHGKHSAAAAGRAPS
                     PPPPGSEAAPSPSKRKRTPSDKSAHTVEHGSPRTRDPTPRPPGLPEEATALAAPSPPR
                     ARARGRGPGLLEPTDAGGPPRSAPEAASMLAAELRGKTRSLGRAEVALGAQGPREKPA
                     PPQKAKRSVPPASPARAPPATETPGPEKAATDLPAPETPRKKTPIQKPPRKKSREAAG
                     ELGRAGAPTL"
     exon            245..303
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            304..405
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            406..925
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            926..1144
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            1145..1273
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            1274..1377
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            1378..1495
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            1496..1611
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            1612..1764
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     exon            1765..3463
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3443..3448
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /note="hexamer: AATAAA"
     polyA_site      3463
                     /gene="SCARF2"
                     /gene_synonym="NSR1; SREC-II; SREC2; SRECRP-1; VDEGS"
                     /note="major polyA site"
ORIGIN      
        1 actccgcttc cggccgctct cgctgcggcc gcacccgcgc ccgtgcccgc cccgcgcctg
       61 ccccgcgcct catggagggc gcagggcccc ggggggccgg gccggcgcgg cgccggggag
      121 ccggggggcc gccgtcaccg ctgctgccgt cgctgctgct gctgctgctg ctctggatgc
      181 tgccggacac cgtggcgcct caggaactga accctcgcgg ccgcaacgtg tgccgtgctc
      241 ccggctccca ggtgcccacg tgctgcgctg gctggaggca gcaaggggac gagtgtggga
      301 ttgcggtgtg cgaaggcaac tccacgtgct cagagaacga ggtgtgcgtg aggcctggcg
      361 agtgccgctg ccgccacggc tacttcggtg ccaactgcga caccaagtgc ccgcgccagt
      421 tctggggccc cgactgcaag gagctgtgta gctgccaccc acacgggcag tgcgaggacg
      481 tgacaggcca gtgtacttgt cacgcgcggc gctggggcgc gcgctgcgag catgcgtgcc
      541 agtgccagca cggcacgtgc cacccgcgga gcggcgcgtg ccgctgtgag cccggctggt
      601 ggggcgcgca gtgcgccagc gcgtgctact gcagcgccac gtcgcgctgc gacccacaga
      661 ccggcgcctg cctgtgccac gcaggctggt ggggccgcag ctgcaacaac cagtgcgcct
      721 gcaactcgtc tccctgcgag cagcagagcg gccgctgtca gtgccgcgag cgtacgttcg
      781 gcgcgcgctg cgatcgctac tgccagtgct tccgcggccg ctgccaccct gtggacggca
      841 cgtgtgcctg cgagccgggc taccgcggca agtactgtcg cgagccgtgc cccgccggct
      901 tctacggctt gggctgtcgc cgccggtgtg gccagtgcaa gggccagcag ccgtgcacgg
      961 tggccgaggg ccgctgcttg acgtgcgagc ccggctggaa cggaaccaag tgcgaccagc
     1021 cttgcgccac cggtttctat ggcgagggct gcagccaccg ctgtccgcca tgccgcgacg
     1081 ggcatgcctg taaccatgtc accggcaagt gtacgcgctg caacgcgggc tggatcggcg
     1141 accggtgcga gaccaagtgt agcaatggca cttacggcga ggactgcgcc ttcgtgtgcg
     1201 ccgactgcgg cagcggacac tgcgacttcc agtcggggcg ctgcctgtgc agccctggcg
     1261 tccacgggcc ccactgtaac gtgacgtgcc cgcccggact ccacggcgcg gactgtgctc
     1321 aggcctgcag ctgccacgag gacacgtgcg acccggtcac tggtgcctgc cacctagaaa
     1381 ccaaccagcg caagggcgtg atgggcgcgg gcgcgctgct cgtcctgctc gtctgcctgc
     1441 tgctctcgct gctcggctgc tgctgcgctt gccgcggcaa ggaccctacg cgccgggagc
     1501 tttcgcttgg gaggaagaag gcgccgcacc gactatgcgg gcgcttcagt cgcatcagca
     1561 tgaagctgcc ccggatcccg ctccggaggc agaaactacc caaagtcgta gtggcccacc
     1621 acgacctgga taacacactc aactgcagct tcctggagcc accctcaggg ctggagcagc
     1681 cctcaccatc ctggtcctct cgggcctcct tctcctcgtt tgacaccact gatgaaggcc
     1741 ctgtgtactg tgtaccccat gaggaggcac cagcggagag ccgggacccc gaagtcccca
     1801 ctgtccctgc cgaggcgccg gcgccgtccc ctgtgccctt gaccacgcca gcctccgccg
     1861 aggaggcgat acccctcccc gcgtcctccg acagcgagcg gtcggcgtcc agcgtggagg
     1921 ggcccggagg ggctctgtac gcgcgcgtgg cccgacgcga ggcccggccg gcccgggccc
     1981 ggggcgagat tgggggcctg tcgctgtcgc catcgcccga gcgcaggaaa ccgccgccac
     2041 ctgaccccgc caccaagcct aaggtgtcct ggatccacgg caagcacagc gccgctgcag
     2101 ctggccgtgc gccctcacca ccgccgccag gctccgaggc cgcgcccagc cccagcaaga
     2161 ggaaacggac gcccagcgac aaatcggcgc atacggtcga acacggcagc ccccggaccc
     2221 gcgacccaac gccgcggccc cccgggctgc ccgaggaggc gacagccctc gctgcgccct
     2281 cgccgcccag ggcccgagcg cggggccgcg gccccggcct cttggagccc acggacgccg
     2341 gcggtccccc gcgaagcgcg cccgaggctg cctccatgtt ggccgctgag ctgcgcggca
     2401 agactcgcag cctgggccgc gccgaggtgg ccctgggcgc gcagggcccc agggaaaagc
     2461 cggcgccccc acagaaagcc aagcgctccg tgccgccagc ctcgcccgcc cgcgcgcccc
     2521 cagcgaccga aaccccgggg cctgagaagg cggcgaccga cttgcccgcg cctgagaccc
     2581 cccggaagaa gacccccatc cagaagccgc cgcgcaagaa gagccgggag gcggcgggcg
     2641 agctgggcag ggcgggcgca cccaccctgt agcaggctgt ggctcgtccg cgcgcagctc
     2701 cctcagcttc gcagcgccgc ccgccacccc acacctccca cgctaccggg cacgggcggc
     2761 ctcctattgg ccgggcaccg cgcggctagc ggaggttgcg tctcattggc tcaggtcctg
     2821 cagccgctcc tggattggag cagtgtgctc tggcgggaag ggcccatccc gttggtcgag
     2881 gcctgacagg cgcttagcgg gcgactccct ccccattggc cgagttatgg agcgctccga
     2941 ccagacagcg tctcattggc caaagatggg agggttccgc ttaaagaccg cctcttactg
     3001 gccaggagtg gacttggtta gggctacctt ctcattggtt gcagccagag gcacttctgc
     3061 ccgggctgcc tctcccccgc tagggcctgg tgcctctggc tggaggctcc ctcccttggc
     3121 cgtcccaata gagcccgggg ctacttccac tggccaggct cccgggcatc tggttgaccc
     3181 cagcctgggg aggagggctg gtctccgctc ctcaggggct tagtccgtcc caccccttcc
     3241 cttccctggc gccccgggcc caggcccctc agctgtcagc tggttttgat ggcctcccac
     3301 tgccccacac gccgcgggac ctccaggggc gactctagtg gcctgaggag atgtatttat
     3361 aggcccccag cagggctgct cccccctcgg ccggtgcccc aggatgggct cctcccggcg
     3421 ggggcttggc caaagctttc ttaataaaat gcctttcccc tca
//
