LOCUS       NM_013439               1271 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens paired immunoglobin like type 2 receptor alpha
            (PILRA), transcript variant 1, mRNA.
ACCESSION   NM_013439
VERSION     NM_013439.3
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 1271)
  AUTHORS   Levi-Monsalve,A., Flores,S.V., Manriquez,G. and Roco-Videla,A.
  TITLE     New candidate SNPs for genetic association with Alzheimer's
            disease: a linkage disequilibrium analysis for the FCGRIIB and
            PILRA genes
  JOURNAL   Medwave 24 (1) (2024)
   PUBMED   38408113
  REMARK    GeneRIF: New candidate SNPs for genetic association with
            Alzheimer's disease: a linkage disequilibrium analysis for the
            FCGRIIB and PILRA genes.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1271)
  AUTHORS   Lopatko Lindman,K., Jonsson,C., Weidung,B., Olsson,J., Pandey,J.P.,
            Prokopenko,D., Tanzi,R.E., Hallmans,G., Eriksson,S., Elgh,F. and
            Lovheim,H.
  TITLE     PILRA polymorphism modifies the effect of APOE4 and GM17 on
            Alzheimer's disease risk
  JOURNAL   Sci Rep 12 (1), 13264 (2022)
   PUBMED   35918447
  REMARK    GeneRIF: PILRA polymorphism modifies the effect of APOE4 and GM17
            on Alzheimer's disease risk.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1271)
  AUTHORS   Zheng,L., Han,X., Yao,S., Zhu,Y., Klement,J., Wu,S., Ji,L., Zhu,G.,
            Cheng,X., Tobiasova,Z., Yu,W., Huang,B., Vesely,M.D., Wang,J.,
            Zhang,J., Quinlan,E. and Chen,L.
  TITLE     The CD8alpha-PILRalpha interaction maintains CD8+ T cell quiescence
  JOURNAL   Science 376 (6596), 996-1001 (2022)
   PUBMED   35617401
  REMARK    GeneRIF: The CD8alpha-PILRalpha interaction maintains CD8(+) T cell
            quiescence.
REFERENCE   4  (bases 1 to 1271)
  AUTHORS   Pandey,J.P., Namboodiri,A.M., Nietert,P.J., Barnes,L.L. and
            Bennett,D.A.
  TITLE     Inhibitory Fcgamma Receptor and Paired Immunoglobulin Type 2
            Receptor Alpha Genotypes in Alzheimer's Disease
  JOURNAL   J Alzheimers Dis 84 (3), 965-968 (2021)
   PUBMED   34602489
  REMARK    GeneRIF: Inhibitory Fcgamma Receptor and Paired Immunoglobulin Type
            2 Receptor Alpha Genotypes in Alzheimer's Disease.
REFERENCE   5  (bases 1 to 1271)
  AUTHORS   Agostini,S., Costa,A.S., Mancuso,R., Guerini,F.R., Nemni,R. and
            Clerici,M.
  TITLE     The PILRA G78R Variant Correlates with Higher HSV-1-Specific IgG
            Titers in Alzheimer's Disease
  JOURNAL   Cell Mol Neurobiol 39 (8), 1217-1221 (2019)
   PUBMED   31297637
  REMARK    GeneRIF: Herpes simplex virus type 1 IgG are increased in
            Alzheimer's disease patients with the protective R78 PILRA
            genotype.
REFERENCE   6  (bases 1 to 1271)
  AUTHORS   Satoh,T., Arii,J., Suenaga,T., Wang,J., Kogure,A., Uehori,J.,
            Arase,N., Shiratori,I., Tanaka,S., Kawaguchi,Y., Spear,P.G.,
            Lanier,L.L. and Arase,H.
  TITLE     PILRalpha is a herpes simplex virus-1 entry coreceptor that
            associates with glycoprotein B
  JOURNAL   Cell 132 (6), 935-944 (2008)
   PUBMED   18358807
  REMARK    GeneRIF: The results demonstrate that cellular receptors for both
            gB and gD are required for HSV-1 infection and that PILRalpha plays
            an important role in HSV-1 infection as a coreceptor that
            associates with gB.
REFERENCE   7  (bases 1 to 1271)
  AUTHORS   Tabata,S., Kuroki,K., Maita,N., Wang,J., Shiratori,I., Arase,H.,
            Kohda,D. and Maenaka,K.
  TITLE     Expression, crystallization and preliminary X-ray diffraction
            analysis of human paired Ig-like type 2 receptor alpha (PILRalpha)
  JOURNAL   Acta Crystallogr Sect F Struct Biol Cryst Commun 64 (Pt 1), 44-46
            (2008)
   PUBMED   18097101
  REMARK    GeneRIF: PILRalpha protein was successfully crystallized at 293 K
            using the sitting-drop vapour-diffusion method and the crystals
            diffracted to 1.3 A resolution.
REFERENCE   8  (bases 1 to 1271)
  AUTHORS   Koga,T., Inui,M., Inoue,K., Kim,S., Suematsu,A., Kobayashi,E.,
            Iwata,T., Ohnishi,H., Matozaki,T., Kodama,T., Taniguchi,T.,
            Takayanagi,H. and Takai,T.
  TITLE     Costimulatory signals mediated by the ITAM motif cooperate with
            RANKL for bone homeostasis
  JOURNAL   Nature 428 (6984), 758-763 (2004)
   PUBMED   15085135
REFERENCE   9  (bases 1 to 1271)
  AUTHORS   Fournier,N., Chalus,L., Durand,I., Garcia,E., Pin,J.J.,
            Churakova,T., Patel,S., Zlot,C., Gorman,D., Zurawski,S., Abrams,J.,
            Bates,E.E. and Garrone,P.
  TITLE     FDF03, a novel inhibitory receptor of the immunoglobulin
            superfamily, is expressed by human dendritic and myeloid cells
  JOURNAL   J Immunol 165 (3), 1197-1209 (2000)
   PUBMED   10903717
REFERENCE   10 (bases 1 to 1271)
  AUTHORS   Mousseau,D.D., Banville,D., L'Abbe,D., Bouchard,P. and Shen,S.H.
  TITLE     PILRalpha, a novel immunoreceptor tyrosine-based inhibitory
            motif-bearing protein, recruits SHP-1 upon tyrosine phosphorylation
            and is paired with the truncated counterpart PILRbeta
  JOURNAL   J Biol Chem 275 (6), 4467-4474 (2000)
   PUBMED   10660620
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC005071.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 26, 2018 this sequence version replaced NM_013439.2.
            
            Summary: Cell signaling pathways rely on a dynamic interaction
            between activating and inhibiting processes. SHP-1-mediated
            dephosphorylation of protein tyrosine residues is central to the
            regulation of several cell signaling pathways. Two types of
            inhibitory receptor superfamily members are immunoreceptor
            tyrosine-based inhibitory motif (ITIM)-bearing receptors and their
            non-ITIM-bearing, activating counterparts. Control of cell
            signaling via SHP-1 is thought to occur through a balance between
            PILRalpha-mediated inhibition and PILRbeta-mediated activation.
            These paired immunoglobulin-like receptor genes are located in a
            tandem head-to-tail orientation on chromosome 7. This particular
            gene encodes the ITIM-bearing member of the receptor pair, which
            functions in the inhibitory role. Alternative splicing has been
            observed at this locus and three variants, each encoding a distinct
            isoform, are described. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF161080.1, SRR5189664.66632.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000198536.7/ ENSP00000198536.2
            RefSeq Select criteria :: based on expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-234               AC005071.2         170793-171026
            235-624             AC005071.2         171350-171739
            625-843             AC005071.2         187194-187412
            844-877             AC005071.2         195185-195218
            878-927             AC005071.2         196597-196646
            928-959             AC005071.2         196887-196918
            960-1271            AC005071.2         197091-197402
FEATURES             Location/Qualifiers
     source          1..1271
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7q22.1"
     gene            1..1271
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="paired immunoglobin like type 2 receptor alpha"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:HGNC:20396"
                     /db_xref="MIM:605341"
     exon            1..234
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     CDS             171..1082
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; cell surface receptor FDF03; inhibitory
                     receptor PILR-alpha"
                     /codon_start=1
                     /product="paired immunoglobulin-like type 2 receptor alpha
                     isoform 1 precursor"
                     /protein_id="NP_038467.2"
                     /db_xref="CCDS:CCDS5691.1"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:HGNC:20396"
                     /db_xref="MIM:605341"
                     /translation="MGRPLLLPLLPLLLPPAFLQPSGSTGSGPSYLYGVTQPKHLSAS
                     MGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWT
                     EGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSITQAVTTTTQRP
                     SSMTTTWRLSSTTTTTGLRVTQGKRRSDSWHISLETAVGVAVAVTVLGIMILGLICLL
                     RWRRRKGQQRTKATTPAREPFQNTEEPYENIRNEGQNTDPKLNPKDDGIVYASLALSS
                     STSPRAPPSHRPLKSPQNETLYSVLKA"
     exon            235..624
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     exon            625..843
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     exon            844..877
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     exon            878..927
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     exon            928..959
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     exon            960..1271
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1250..1255
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="hexamer: AATAAA"
     polyA_site      1271
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="major polyA site"
ORIGIN      
        1 accctggagg tgcactggtt tggggaaggc tcctggcccc cacagccctc ttcggagcct
       61 gagcccggct ctcctcactc acctcaaccc ccaggcggcc cctccacagg gcccctctcc
      121 tgcctggacg gctctgctgg tctccccgtc ccctggagaa gaacaaggcc atgggtcggc
      181 ccctgctgct gcccctactg cccttgctgc tgccgccagc atttctgcag cctagtggct
      241 ccacaggatc tggtccaagc tacctttatg gggtcactca accaaaacac ctctcagcct
      301 ccatgggtgg ctctgtggaa atccccttct ccttctatta cccctgggag ttagccacag
      361 ctcccgacgt gagaatatcc tggagacggg gccacttcca caggcagtcc ttctacagca
      421 caaggccgcc ttccattcac aaggattatg tgaaccggct ctttctgaac tggacagagg
      481 gtcagaagag cggcttcctc aggatctcca acctgcagaa gcaggaccag tctgtgtatt
      541 tctgccgagt tgagctggac acacggagct cagggaggca gcagtggcag tccatcgagg
      601 ggaccaaact ctccatcacc caggctgtca cgaccaccac ccagaggccc agcagcatga
      661 ctaccacctg gaggctcagt agcacaacca ccacaaccgg cctcagggtc acacagggca
      721 aacgacgctc agactcttgg cacataagtc tggagactgc tgtgggggtg gcagtggctg
      781 tcactgtgct cggaatcatg attttgggac tgatctgcct cctcaggtgg aggagaagga
      841 aaggtcagca gcggactaaa gccacaaccc cagccaggga acccttccaa aacacagagg
      901 agccatatga gaatatcagg aatgaaggac aaaatacaga tcccaagcta aatcccaagg
      961 atgacggcat cgtctatgct tcccttgccc tctccagctc cacctcaccc agagcacctc
     1021 ccagccaccg tcccctcaag agcccccaga acgagaccct gtactctgtc ttaaaggcct
     1081 aaccaatgga cagccctctc aagactgaat ggtgaggcca ggtacagtgg cgcacacctg
     1141 taatcccagc tactctgaag cctgaggcag aatcaagtga gcccaggagt tcagggccag
     1201 ctttgataat ggagcgagat gccatctcta gttaaaaata tatattaaca ataaagtaac
     1261 aaatttaaaa a
//
