LOCUS       NM_001127207            3070 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens SNF2 related chromatin remodeling annealing helicase 1
            (SMARCAL1), transcript variant 2, mRNA.
ACCESSION   NM_001127207
VERSION     NM_001127207.2
KEYWORDS    RefSeq.
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 3070)
  AUTHORS   Sun,B.B., Wang,G.Z., Han,S.C., Yang,F.Y., Guo,H., Liu,J., Liu,Y.T.
            and Zhou,G.B.
  TITLE     Oncogenic functions and therapeutic potentials of targeted
            inhibition of SMARCAL1 in small cell lung cancer
  JOURNAL   Cancer Lett 592, 216929 (2024)
   PUBMED   38697461
  REMARK    GeneRIF: Oncogenic functions and therapeutic potentials of targeted
            inhibition of SMARCAL1 in small cell lung cancer.
REFERENCE   2  (bases 1 to 3070)
  AUTHORS   Batenburg,N.L., Sowa,D.J., Walker,J.R., Andres,S.N. and Zhu,X.D.
  TITLE     CSB and SMARCAL1 compete for RPA32 at stalled forks and
            differentially control the fate of stalled forks in BRCA2-deficient
            cells
  JOURNAL   Nucleic Acids Res 52 (9), 5067-5087 (2024)
   PUBMED   38416570
  REMARK    GeneRIF: CSB and SMARCAL1 compete for RPA32 at stalled forks and
            differentially control the fate of stalled forks in BRCA2-deficient
            cells.
REFERENCE   3  (bases 1 to 3070)
  AUTHORS   Liu,H., Xu,C., Diplas,B.H., Brown,A., Strickland,L.M., Yao,H.,
            Ling,J., McLendon,R.E., Keir,S.T., Ashley,D.M., He,Y. and
            Waitkus,M.S.
  TITLE     Cancer-associated SMARCAL1 loss-of-function mutations promote
            alternative lengthening of telomeres and tumorigenesis in
            telomerase-negative glioblastoma cells
  JOURNAL   Neuro Oncol 25 (9), 1563-1575 (2023)
   PUBMED   36689342
  REMARK    GeneRIF: Cancer-associated SMARCAL1 loss-of-function mutations
            promote alternative lengthening of telomeres and tumorigenesis in
            telomerase-negative glioblastoma cells.
            Erratum:[Neuro Oncol. 2023 Nov 2;25(11):2105. doi:
            10.1093/neuonc/noad180.. PMID: 37757453]
REFERENCE   4  (bases 1 to 3070)
  AUTHORS   Castellano-Martinez,A., Acunas-Soto,S., Varga-Martinez,R.,
            Rodriguez-Gonzalez,M., Mora-Lopez,F., Iriarte-Gahete,M. and
            Roldan-Cano,V.
  TITLE     Different Phenotypes of Schimke Immuno-Osseous Dysplasia (SIOD) in
            Two Sisters with the Same Mutation in the SMARCAL1 Gene
  JOURNAL   Endocr Metab Immune Disord Drug Targets 22 (8), 888-894 (2022)
   PUBMED   35209826
  REMARK    GeneRIF: Different Phenotypes of Schimke Immuno-Osseous Dysplasia
            (SIOD) in Two Sisters with the Same Mutation in the SMARCAL1 Gene.
REFERENCE   5  (bases 1 to 3070)
  AUTHORS   Brosnan-Cashman,J.A., Davis,C.M., Diplas,B.H., Meeker,A.K.,
            Rodriguez,F.J. and Heaphy,C.M.
  TITLE     SMARCAL1 loss and alternative lengthening of telomeres (ALT) are
            enriched in giant cell glioblastoma
  JOURNAL   Mod Pathol 34 (10), 1810-1819 (2021)
   PUBMED   34103668
  REMARK    GeneRIF: SMARCAL1 loss and alternative lengthening of telomeres
            (ALT) are enriched in giant cell glioblastoma.
REFERENCE   6  (bases 1 to 3070)
  AUTHORS   Bokenkamp,A., deJong,M., van Wijk,J.A., Block,D., van Hagen,J.M.
            and Ludwig,M.
  TITLE     R561C missense mutation in the SMARCAL1 gene associated with mild
            Schimke immuno-osseous dysplasia
  JOURNAL   Pediatr Nephrol 20 (12), 1724-1728 (2005)
   PUBMED   16237566
  REMARK    GeneRIF: Missense mutation in the SMARCAL1 gene is associated with
            mild Schimke immuno-osseous dysplasia.
REFERENCE   7  (bases 1 to 3070)
  AUTHORS   Lou,S., Lamfers,P., McGuire,N. and Boerkoel,C.F.
  TITLE     Longevity in Schimke immuno-osseous dysplasia
  JOURNAL   J Med Genet 39 (12), 922-925 (2002)
   PUBMED   12471207
  REMARK    GeneRIF: Schimke immuno-osseous dysplasia: a patient who has
            survived to 20 years despite having a homozygous SMARCAL1 nonsense
            mutation and severe early onset disease
REFERENCE   8  (bases 1 to 3070)
  AUTHORS   Boerkoel,C.F., Takashima,H., John,J., Yan,J., Stankiewicz,P.,
            Rosenbarker,L., Andre,J.L., Bogdanovic,R., Burguet,A.,
            Cockfield,S., Cordeiro,I., Frund,S., Illies,F., Joseph,M.,
            Kaitila,I., Lama,G., Loirat,C., McLeod,D.R., Milford,D.V.,
            Petty,E.M., Rodrigo,F., Saraiva,J.M., Schmidt,B., Smith,G.C.,
            Spranger,J., Stein,A., Thiele,H., Tizard,J., Weksberg,R.,
            Lupski,J.R. and Stockton,D.W.
  TITLE     Mutant chromatin remodeling protein SMARCAL1 causes Schimke
            immuno-osseous dysplasia
  JOURNAL   Nat Genet 30 (2), 215-220 (2002)
   PUBMED   11799392
REFERENCE   9  (bases 1 to 3070)
  AUTHORS   Coleman,M.A., Eisen,J.A. and Mohrenweiser,H.W.
  TITLE     Cloning and characterization of HARP/SMARCAL1: a prokaryotic
            HepA-related SNF2 helicase protein from human and mouse
  JOURNAL   Genomics 65 (3), 274-282 (2000)
   PUBMED   10857751
REFERENCE   10 (bases 1 to 3070)
  AUTHORS   Lippner,E., Lucke,T., Salgado,C., Boerkoel,C. and Lewis,D.B.
  TITLE     Schimke Immunoosseous Dysplasia
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301550
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA856812.1, BC043341.1 and
            BX104166.1.
            
            On Jun 2, 2019 this sequence version replaced NM_001127207.1.
            
            Summary: The protein encoded by this gene is a member of the
            SWI/SNF family of proteins. Members of this family have helicase
            and ATPase activities and are thought to regulate transcription of
            certain genes by altering the chromatin structure around those
            genes. The encoded protein shows sequence similarity to the E. coli
            RNA polymerase-binding protein HepA. Mutations in this gene are a
            cause of Schimke immunoosseous dysplasia (SIOD), an autosomal
            recessive disorder with the diagnostic features of
            spondyloepiphyseal dysplasia, renal dysfunction, and T-cell
            immunodeficiency. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) differs in the 5' UTR,
            compared to variant 1. Variants 1 and 2 encode the same protein.
            
            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 :: BC043341.1, SRR1803611.46485.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-550               DA856812.1         16-565
            551-3045            BC043341.1         539-3033
            3046-3070           BX104166.1         11-35               c
FEATURES             Location/Qualifiers
     source          1..3070
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q35"
     gene            1..3070
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="SNF2 related chromatin remodeling annealing
                     helicase 1"
                     /db_xref="GeneID:50485"
                     /db_xref="HGNC:HGNC:11102"
                     /db_xref="MIM:606622"
     exon            1..34
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            35..71
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            72..940
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     CDS             130..2994
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="ATP-driven annealing helicase; HepA-related
                     protein; SMARCA-like protein 1; sucrose nonfermenting
                     protein 2-like 1; SWI/SNF related, matrix associated,
                     actin dependent regulator of chromatin, subfamily a like
                     1"
                     /codon_start=1
                     /product="SWI/SNF-related matrix-associated
                     actin-dependent regulator of chromatin subfamily A-like
                     protein 1"
                     /protein_id="NP_001120679.1"
                     /db_xref="CCDS:CCDS2403.1"
                     /db_xref="GeneID:50485"
                     /db_xref="HGNC:HGNC:11102"
                     /db_xref="MIM:606622"
                     /translation="MSLPLTEEQRKKIEENRQKALARRAEKLLAEQHQRTSSGTSIAG
                     NPFQAKQGPSQNFPRESCKPVSHGVIFKQQNLSSSSNADQRPHDSHSFQAKGIWKKPE
                     EMPTACPGHSPRSQMALTGISPPLAQSPPEVPKQQLLSYELGQGHAQASPEIRFTPFA
                     NPTHKPLAKPKSSQETPAHSSGQPPRDAKLEAKTAKASPSGQNISYIHSSSESVTPRT
                     EGRLQQKSGSSVQKGVNSQKGKCVRNGDRFQVLIGYNAELIAVFKTLPSKNYDPDTKT
                     WNFSMNDYSALMKAAQSLPTVNLQPLEWAYGSSESPSTSSEGQAGLPSAPSLSFVKGR
                     CMLISRAYFEADISYSQDLIALFKQMDSRRYDVKTRKWSFLLEEHSKLIAKVRCLPQV
                     QLDPLPTTLTLAFASQLKKTSLSLTPDVPEADLSEVDPKLVSNLMPFQRAGVNFAIAK
                     GGRLLLADDMGLGKTIQAICIAAFYRKEWPLLVVVPSSVRFTWEQAFLRWLPSLSPDC
                     INVVVTGKDRLTAGLINIVSFDLLSKLEKQLKTPFKVVIIDESHFLKNSRTARCRAAM
                     PVLKVAKRVILLSGTPAMSRPAELYTQIIAVKPTFFPQFHAFGLRYCDAKRMPWGWDY
                     SGSSNLGELKLLLEEAVMLRRLKSDVLSQLPAKQRKIVVIAPGRINARTRAALDAAAK
                     EMTTKDKTKQQQKDALILFFNRTAEAKIPSVIEYILDLLESGREKFLVFAHHKVVLDA
                     ITQELERKHVQHIRIDGSTSSAEREDLCQQFQLSERHAVAVLSITAANMGLTFSSADL
                     VVFAELFWNPGVLIQAEDRVHRIGQTSSVGIHYLVAKGTADDYLWPLIQEKIKVLAEA
                     GLSETNFSEMTESTDYLYKDPKQQKIYDLFQKSFEKEGSDMELLEAAESFDPGSASGT
                     SGSSSQNMGDTLDESSLTASPQKKRRFEFFDNWDSFTSPL"
     exon            941..991
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            992..1225
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1226..1276
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1277..1463
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1464..1614
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1615..1773
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1774..1839
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1840..1980
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1981..2199
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2200..2270
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2271..2373
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2374..2556
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2557..2657
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2658..2754
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2755..3070
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3013..3018
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="hexamer: AATAAA"
     polyA_site      3034
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
     regulatory      3049..3054
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="hexamer: AATAAT"
     polyA_site      3070
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="major polyA site"
ORIGIN      
        1 agtggggcgt ggcgcccgct taccttgagg ctgggttgga aaaagactat gttagcaagt
       61 gtcacgccat gcttttgcca actttccaat taaaggttga cattcctgca taagcatttc
      121 tctgtgaaaa tgtccttgcc tcttacagag gagcagagga aaaagattga agagaatcga
      181 caaaaggctc tggcccgcag agctgagaag ttattggcag aacagcatca gaggactagc
      241 tcgggcacct ccattgctgg caacccattc caggccaagc aaggcccatc ccaaaatttc
      301 ccaagggagt cttgtaagcc agtgagccat ggtgtcattt tcaagcaaca gaatctcagt
      361 agctcatcta atgctgacca aagacctcat gattcccaca gttttcaggc aaagggaata
      421 tggaaaaagc cagaagaaat gcccacagcc tgcccaggcc acagtccacg tagtcaaatg
      481 gctctcactg gaatctctcc tcccttggca caaagtcctc cagaggtccc taaacaacag
      541 ctcttgagtt atgagttagg tcaaggtcat gctcaggctt cacctgagat caggttcaca
      601 ccctttgcta acccaactca taagcctctg gccaaaccaa agagttccca agagacacca
      661 gctcattcct ctggacagcc tcccagggat gctaagttag aggccaagac agcaaaagcc
      721 tccccttcgg ggcagaacat ttcttacatc cattctagct cagagagtgt aacgcccagg
      781 acagaaggaa gactccagca gaagtcaggg tcctcagtcc aaaaaggagt gaactctcag
      841 aagggaaagt gcgtaaggaa cggcgatcgt ttccaggtgt tgattgggta caatgcggaa
      901 ctcattgcag tgtttaagac cctgcccagc aagaattatg atcctgacac caagacgtgg
      961 aacttcagca tgaatgacta tagtgccctg atgaaagcag cccagagcct ccccacggtc
     1021 aacctgcagc ctctggaatg ggcctatggc agcagcgagt caccctccac cagcagtgag
     1081 ggacaggccg gccttccatc agctccatcc ctttcatttg tcaaagggcg atgcatgctc
     1141 atctccaggg cctacttcga ggcagacatc agttattcac aggaccttat tgcgcttttt
     1201 aaacagatgg attccagaag atatgatgtc aagaccagga agtggagctt tctcttggaa
     1261 gagcacagta aactaattgc aaaggtgcgc tgcctcccac aagttcagct ggaccctctg
     1321 cccacgactc tcaccctggc gtttgcttct cagctcaaga agacatctct cagtctcacg
     1381 ccagatgtcc cagaggcaga cctttctgaa gtggacccca agctcgtgtc taatctgatg
     1441 ccctttcaga gagctggagt caattttgcc atagccaaag gaggccgcct gctgctcgct
     1501 gacgacatgg gcctggggaa gaccatccaa gccatctgca tcgcagcctt ttaccggaag
     1561 gagtggccgc tcctggtggt ggtgccatcc tccgtgcgct tcacctggga gcaggccttc
     1621 cttcggtggc tgccatctct gagcccagat tgcatcaacg tcgtggtgac tgggaaggac
     1681 cgcctgacag ctggcctgat caacattgtc agctttgacc ttcttagcaa gttggaaaaa
     1741 cagctaaaaa ccccttttaa agttgtcatc attgatgaat ctcacttcct caaaaacagt
     1801 aggactgccc gctgtcgagc agctatgccg gtcctaaagg ttgccaagag ggtgatcctg
     1861 ttgtcgggca caccagccat gtcccggccc gcagagctct acacgcagat catcgcagtc
     1921 aagccaactt tcttccccca gtttcatgcc tttggacttc gctactgtga tgccaaacgg
     1981 atgccttggg ggtgggacta ctcaggttcc tccaacctgg gagagctgaa gctcctgctg
     2041 gaggaagcag tcatgctgcg gcgcctcaag tccgacgtcc tttcccagct gcctgccaag
     2101 cagcgcaaga tagtggtgat tgccccagga cggatcaatg ccaggaccag agctgccctg
     2161 gatgctgcag ccaaggaaat gaccaccaag gacaaaacta aacagcagca gaaagatgcc
     2221 ctcattctct tcttcaacag aacagctgaa gctaaaatcc catctgtcat tgaatatatc
     2281 ttggacctac tggaaagtgg aagagagaag tttttagtat ttgcacacca taaggtggtc
     2341 ctggacgcaa ttacgcaaga gcttgagaga aagcacgtgc agcacatccg catcgatggc
     2401 tccacctcat cagctgagcg ggaggacctg tgccagcagt tccaactgtc ggagaggcat
     2461 gctgtggccg tgctgtccat caccgctgcc aatatgggcc tcaccttctc ctcggctgac
     2521 ctggtggtgt ttgctgagct gttttggaac ccaggggtgc tgatccaggc tgaggaccgc
     2581 gtgcaccgca ttggacagac cagctccgtg ggcattcact acctcgtggc aaagggcaca
     2641 gctgatgact acctttggcc cctgattcaa gagaagatta aagttctggc agaagccggg
     2701 ctttctgaga ccaatttttc agaaatgaca gaatccactg attacctcta caaggaccca
     2761 aagcagcaga agatctacga cctattccag aagtcctttg agaaagaagg aagtgatatg
     2821 gagctcctgg aagcagcaga gtcctttgac ccaggaagtg cttcaggaac atctggaagt
     2881 agttcccaga acatgggaga caccctggat gaaagctcat tgacagccag tccacagaag
     2941 aaaaggagat ttgaattttt tgataactgg gacagcttta cgtctcccct gtaaaagggg
     3001 caaaaagaaa aaaataaaaa gcattttaaa atcatggaat tgaaataaaa taatgtattt
     3061 tgttttaaaa
//
