LOCUS       NM_015967               3607 bp    mRNA    linear   PRI 24-OCT-2024
DEFINITION  Homo sapiens protein tyrosine phosphatase non-receptor type 22
            (PTPN22), transcript variant 1, mRNA.
ACCESSION   NM_015967
VERSION     NM_015967.8
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 3607)
  AUTHORS   Jabeen,A., Riaz,S., Usman,M., Parveen,A., Mukhtar,M., Wajid,A.,
            Hanif,A. and Batool,A.
  TITLE     Association of polymorphism of NLRP3, ICAM-1, PTPN22, INS genes in
            childhood onset type 1 diabetes in a Pakistani population
  JOURNAL   Mol Biol Rep 51 (1), 1070 (2024)
   PUBMED   39425874
  REMARK    GeneRIF: Association of polymorphism of NLRP3, ICAM-1, PTPN22, INS
            genes in childhood onset type 1 diabetes in a Pakistani population.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3607)
  AUTHORS   Ruiz-Martin,V., Marcos,T., de Pereda,J.M., Sanchez-Crespo,M., de la
            Fuente,M.A., Bayon,Y. and Alonso,A.
  TITLE     LYP regulates SLP76 and other adaptor proteins in T cells
  JOURNAL   Biol Res 57 (1), 69 (2024)
   PUBMED   39342392
  REMARK    GeneRIF: LYP regulates SLP76 and other adaptor proteins in T cells.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3607)
  AUTHORS   Zhuang,C., Yang,S., Gonzalez,C.G., Ainsworth,R.I., Li,S.,
            Kobayashi,M.T., Wierzbicki,I., Rossitto,L.M., Wen,Y., Peti,W.,
            Stanford,S.M., Gonzalez,D.J., Murali,R., Santelli,E. and Bottini,N.
  TITLE     A novel gain-of-function phosphorylation site modulates PTPN22
            inhibition of TCR signaling
  JOURNAL   J Biol Chem 300 (6), 107393 (2024)
   PUBMED   38777143
  REMARK    GeneRIF: A novel gain-of-function phosphorylation site modulates
            PTPN22 inhibition of TCR signaling.
REFERENCE   4  (bases 1 to 3607)
  AUTHORS   Liu,M., Xia,N., Zha,L., Yang,H., Gu,M., Hao,Z., Zhu,X., Li,N.,
            He,J., Tang,T., Nie,S., Zhang,M., Lv,B., Lu,Y., Jiao,J., Li,J. and
            Cheng,X.
  TITLE     Increased expression of protein tyrosine phosphatase nonreceptor
            type 22 alters early T-cell receptor signaling and differentiation
            of CD4+ T cells in chronic heart failure
  JOURNAL   FASEB J 38 (1), e23386 (2024)
   PUBMED   38112398
  REMARK    GeneRIF: Increased expression of protein tyrosine phosphatase
            nonreceptor type 22 alters early T-cell receptor signaling and
            differentiation of CD4[+] T cells in chronic heart failure.
REFERENCE   5  (bases 1 to 3607)
  AUTHORS   Sakalyte,R., Stropuviene,S., Jasionyte,G., Bagdonaite,L. and
            Venalis,A.
  TITLE     Association between PYTPN22 rs2476601, VEGF rs833070, TNFAIP3
            rs6920220 Polymorphisms and Risk for Rheumatoid Arthritis in Early
            Undifferentiated Arthritis Patients: A Pilot Study
  JOURNAL   Medicina (Kaunas) 59 (10), 1824 (2023)
   PUBMED   37893542
  REMARK    GeneRIF: Association between PYTPN22 rs2476601, VEGF rs833070,
            TNFAIP3 rs6920220 Polymorphisms and Risk for Rheumatoid Arthritis
            in Early Undifferentiated Arthritis Patients: A Pilot Study.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3607)
  AUTHORS   Chien,W., Tidow,N., Williamson,E.A., Shih,L.Y., Krug,U.,
            Kettenbach,A., Fermin,A.C., Roifman,C.M. and Koeffler,H.P.
  TITLE     Characterization of a myeloid tyrosine phosphatase, Lyp, and its
            role in the Bcr-Abl signal transduction pathway
  JOURNAL   J Biol Chem 278 (30), 27413-27420 (2003)
   PUBMED   12764153
  REMARK    GeneRIF: Lyp may play an antagonistic role in signaling by the
            Bcr-Abl fusion protein
REFERENCE   7  (bases 1 to 3607)
  AUTHORS   Hill,R.J., Zozulya,S., Lu,Y.L., Ward,K., Gishizky,M. and Jallal,B.
  TITLE     The lymphoid protein tyrosine phosphatase Lyp interacts with the
            adaptor molecule Grb2 and functions as a negative regulator of
            T-cell activation
  JOURNAL   Exp Hematol 30 (3), 237-244 (2002)
   PUBMED   11882361
  REMARK    GeneRIF: data demonstrate a novel interaction between Lyp and the
            adaptor Grb2 and are consistent with a negative regulatory role for
            Lyp in T-cell signaling.
REFERENCE   8  (bases 1 to 3607)
  AUTHORS   Gjorloff-Wingren,A., Saxena,M., Han,S., Wang,X., Alonso,A.,
            Renedo,M., Oh,P., Williams,S., Schnitzer,J. and Mustelin,T.
  TITLE     Subcellular localization of intracellular protein tyrosine
            phosphatases in T cells
  JOURNAL   Eur J Immunol 30 (8), 2412-2421 (2000)
   PUBMED   10940933
REFERENCE   9  (bases 1 to 3607)
  AUTHORS   Cohen,S., Dadi,H., Shaoul,E., Sharfe,N. and Roifman,C.M.
  TITLE     Cloning and characterization of a lymphoid-specific, inducible
            human protein tyrosine phosphatase, Lyp
  JOURNAL   Blood 93 (6), 2013-2024 (1999)
   PUBMED   10068674
REFERENCE   10 (bases 1 to 3607)
  AUTHORS   Matthews,R.J., Bowne,D.B., Flores,E. and Thomas,M.L.
  TITLE     Characterization of hematopoietic intracellular protein tyrosine
            phosphatases: description of a phosphatase containing an SH2 domain
            and another enriched in proline-, glutamic acid-, serine-, and
            threonine-rich sequences
  JOURNAL   Mol Cell Biol 12 (5), 2396-2405 (1992)
   PUBMED   1373816
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB145424.1, AF077031.1,
            AL137856.24, BC071670.1, AF001846.1 and AA836401.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jan 24, 2022 this sequence version replaced NM_015967.7.
            
            Summary: This gene encodes of member of the non-receptor class 4
            subfamily of the protein-tyrosine phosphatase family. The encoded
            protein is a lymphoid-specific intracellular phosphatase that
            associates with the molecular adapter protein CBL and may be
            involved in regulating CBL function in the T-cell receptor
            signaling pathway. Mutations in this gene may be associated with a
            range of autoimmune disorders including Type 1 Diabetes, rheumatoid
            arthritis, systemic lupus erythematosus and Graves' disease.
            Alternatively spliced transcript variants encoding distinct
            isoforms have been described. [provided by RefSeq, Mar 2009].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            Sequence Note:.
            
            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 :: AF077031.1, AF001846.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000359785.10/ ENSP00000352833.5
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-17                DB145424.1         42-58
            18-465              AF077031.1         1-448
            466-144083          AL137856.24        1-143618
            144084-144145       AF077031.1         450-511
            144146-287763       AL137856.24        1-143618
            287764-288581       AF077031.1         513-1330
            288582-432199       AL137856.24        1-143618
            432200-432797       AF077031.1         1332-1929
            432798-576415       AL137856.24        1-143618
            576416-576780       AF077031.1         1931-2295
            576781-720398       AL137856.24        1-143618
            720399-720598       AF077031.1         2297-2496
            720599-720913       BC071670.1         2335-2649
            720914-720914       AF001846.1         2776-2776
            720915-721688       BC071670.1         2651-3424
            721689-721692       AA836401.1         25-28               c
FEATURES             Location/Qualifiers
     source          1..3607
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p13.2"
     gene            1..3607
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /note="protein tyrosine phosphatase non-receptor type 22"
                     /db_xref="GeneID:26191"
                     /db_xref="HGNC:HGNC:9652"
                     /db_xref="MIM:600716"
     exon            1..176
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     CDS             90..2513
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /EC_number="3.1.3.48"
                     /note="isoform 1 is encoded by transcript variant 1;
                     lymphoid-specific protein tyrosine phosphatase;
                     PEST-domain phosphatase; protein tyrosine phosphatase,
                     non-receptor type 8; hematopoietic cell protein-tyrosine
                     phosphatase 70Z-PEP; protein tyrosine phosphatase,
                     non-receptor type 22 (lymphoid)"
                     /codon_start=1
                     /product="tyrosine-protein phosphatase non-receptor type
                     22 isoform 1"
                     /protein_id="NP_057051.4"
                     /db_xref="CCDS:CCDS863.1"
                     /db_xref="GeneID:26191"
                     /db_xref="HGNC:HGNC:9652"
                     /db_xref="MIM:600716"
                     /translation="MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTY
                     PTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIAT
                     QGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSC
                     EAEKRKSDYIIRTLKVKFNSETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQED
                     DSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQ
                     EQYELVYNAVLELFKRQMDVIRDKHSGTESQAKHCIPEKNHTLQADSYSPNLPKSTTK
                     AAKMMNQQRTKMEIKESSSFDFRTSEISAKEELVLHPAKSSTSFDFLELNYSFDKNAD
                     TTMKWQTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKST
                     PFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDSKHQ
                     IRNASNVKHHDSSALGVYSYIPLVENPYFSSWPPSGTSSKMSLDLPEKQDGTVFPSSL
                     LPTSSTSLFSYYNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVWTPES
                     FIVVEEAGEFSPNVPKSLSSAVKVKIGTSLEWGGTSEPKKFDDSVILRPSKSVKLRSP
                     KSELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLK
                     TPGKSFTRSKSLKILRNMKKSICNSCPPNKPAESVQSNNSSSFLNFGFANRFSKPKGP
                     RNPPPTWNI"
     exon            177..285
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            286..362
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            363..458
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            459..497
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            498..569
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            570..629
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            630..772
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            773..839
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            840..917
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            918..1004
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            1005..1081
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            1082..1899
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            1900..1983
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            1984..2114
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            2115..2142
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            2143..2223
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            2224..2339
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            2340..2370
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            2371..2448
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     exon            2449..3607
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3582..3587
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /note="hexamer: AATAAA"
     polyA_site      3607
                     /gene="PTPN22"
                     /gene_synonym="LYP; LYP1; LYP2; PEP; PTPN22.5; PTPN22.6;
                     PTPN8"
                     /note="major polyA site"
ORIGIN      
        1 agtggctttt tggaggtgtc tcggccatga cacacatttg acatgccctc cctcaaccta
       61 cttatagact atttttcttg ctctgcagca tggaccaaag agaaattctg cagaagttcc
      121 tggatgaggc ccaaagcaag aaaattacta aagaggagtt tgccaatgaa tttctgaagc
      181 tgaaaaggca atctaccaag tacaaggcag acaaaaccta tcctacaact gtggctgaga
      241 agcccaagaa tatcaagaaa aacagatata aggatatttt gccctatgat tatagccggg
      301 tagaactatc cctgataacc tctgatgagg attccagcta catcaatgcc aacttcatta
      361 agggagttta tggacccaag gcttatattg ccacccaggg tcctttatct acaaccctcc
      421 tggacttctg gaggatgatt tgggaatata gtgtccttat cattgttatg gcatgcatgg
      481 agtatgaaat gggaaagaaa aagtgtgagc gctactgggc tgagccagga gagatgcagc
      541 tggaatttgg ccctttctct gtatcctgtg aagctgaaaa aaggaaatct gattatataa
      601 tcaggactct aaaagttaag ttcaatagtg aaactcgaac tatctaccag tttcattaca
      661 agaattggcc agaccatgat gtaccttcat ctatagaccc tattcttgag ctcatctggg
      721 atgtacgttg ttaccaagag gatgacagtg ttcccatatg cattcactgc agtgctggct
      781 gtggaaggac tggtgttatt tgtgctattg attatacatg gatgttgcta aaagatggga
      841 taattcctga gaacttcagt gttttcagtt tgatccggga aatgcggaca cagaggcctt
      901 cattagttca aacgcaggaa caatatgaac tggtctacaa tgctgtatta gaactattta
      961 agagacagat ggatgttatc agagataaac attctggaac agagagtcaa gcaaagcatt
     1021 gtattcctga gaaaaatcac actctccaag cagactctta ttctcctaat ttaccaaaaa
     1081 gtaccacaaa agcagcaaaa atgatgaacc aacaaaggac aaaaatggaa atcaaagaat
     1141 cttcttcctt tgactttagg acttctgaaa taagtgcaaa agaagagcta gttttgcacc
     1201 ctgctaaatc aagcacttct tttgactttc tggagctaaa ttacagtttt gacaaaaatg
     1261 ctgacacaac catgaaatgg cagacaaagg catttccaat agttggggag cctcttcaga
     1321 agcatcaaag tttggatttg ggctctcttt tgtttgaggg atgttctaat tctaaacctg
     1381 taaatgcagc aggaagatat tttaattcaa aggtgccaat aacacggacc aaatcaactc
     1441 cttttgaatt gatacagcag agagaaacca aggaggtgga cagcaaggaa aacttttctt
     1501 atttggaatc tcaaccacat gattcttgtt ttgtagagat gcaggctcaa aaagtaatgc
     1561 atgtttcttc agcagaactg aattattcac tgccatatga ctctaaacac caaatacgta
     1621 atgcctctaa tgtaaagcac catgactcta gtgctcttgg tgtatattct tacatacctt
     1681 tagtggaaaa tccttatttt tcatcatggc ctccaagtgg taccagttct aagatgtctc
     1741 ttgatttacc tgagaagcaa gatggaactg tttttccttc ttctctgttg ccaacatcct
     1801 ctacatccct cttctcttat tacaattcac atgattcttt atcactgaat tctccaacca
     1861 atatttcctc actattgaac caggagtcag ctgtactagc aactgctcca aggatagatg
     1921 atgaaatccc ccctccactt cctgtatgga cacctgaatc atttattgtg gttgaggaag
     1981 ctggagaatt ctcaccaaat gttcccaaat ccttatcctc agctgtgaag gtaaaaattg
     2041 gaacatcact ggaatggggt ggaacatctg aaccaaagaa atttgatgac tctgtgatac
     2101 ttagaccaag caagagtgta aaactccgaa gtcctaaatc agaactacat caagatcgtt
     2161 cttctccccc acctcctctc ccagaaagaa ctctagagtc cttctttctt gccgatgaag
     2221 attgtatgca ggcccaatct atagaaacat attctactag ctatcctgac accatggaaa
     2281 attcaacatc ttcaaaacag acactgaaga ctcctggaaa aagtttcaca aggagtaaga
     2341 gtttgaaaat tttgcgaaac atgaaaaaga gtatctgtaa ttcttgccca ccaaacaagc
     2401 ctgcagaatc tgttcagtca aataactcca gctcatttct gaattttggt tttgcaaacc
     2461 gtttttcaaa acccaaagga ccaaggaatc caccaccaac ttggaatatt taataaaact
     2521 ccagatttat aataatatgg gctgcaagta cacctgcaaa taaaactact agaatactgc
     2581 tagttaaaat aagtgctcta tatgcataat atcaaatatg aagatatgct aatgtgttaa
     2641 tagcttttaa aagaaaagca aaatgccaat aagtgccagt tttgcatttt catatcattt
     2701 gcattgagtt gaaaactgca aataaaagtt tgtcacttga gcttatgtac agaatgctat
     2761 atgagaaaca cttttagaat ggatttattt ttcatttttg ccagttattt ttattttctt
     2821 ttacttttct acataaacat aaacttcaaa aggtttgtaa gatttggatc tcaactaatt
     2881 tctacattgc cagaatatac tataaaaagt taaaaaaaaa acttactttg tgggttgcaa
     2941 tacaaactgc tcttgacaat gactattccc tgacagttat ttttgcctaa atggagtata
     3001 ccttgtaaat cttcccaaat gttgtggaaa actggaatat taagaaaatg agaaattata
     3061 tttattagaa taaaatgtgc aaataatgac aattatttga atgtaacaag gaattcaact
     3121 gaaatcctga taagttttaa ccaaagtcat taaattacca attctagaaa agtaatcaat
     3181 gaaatataat agctatcttt tggtagcaaa agatataaat tgtatatgtt tatacaggat
     3241 ctttcagatc atgtgcaatt tttatctaac caatcagaaa tactagttta aaatgaattt
     3301 ctatatgaat atggatctgc cataagaaaa tctagttcaa ctctaatttt atgtagtaaa
     3361 taaattggca ggtaattgtt tttacaaaga atccacctga cttcccctaa tgcattaaaa
     3421 atatttttat ttaaataact ttatttataa cttttagaaa catgtagtat tgtttaaaca
     3481 tcatttgttc ttcagtattt ttcatttgga agtccaatag ggcaaattga atgaagtatt
     3541 attatctgtc tcttgtagta caatgtatcc aacagacact caataaactt tttggttgtt
     3601 aaactga
//
