LOCUS       NM_014140               3201 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens SNF2 related chromatin remodeling annealing helicase 1
            (SMARCAL1), transcript variant 1, mRNA.
ACCESSION   NM_014140
VERSION     NM_014140.4
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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 3201)
  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 DB099423.1, BC043341.1 and
            BX104166.1.
            
            On Aug 31, 2019 this sequence version replaced NM_014140.3.
            
            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 (1) represents the longer
            transcript. 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 :: AK023780.1, SRR18074969.3226927.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000357276.9/ ENSP00000349823.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-528               DB099423.1         71-598
            529-3176            BC043341.1         386-3033
            3177-3201           BX104166.1         11-35               c
FEATURES             Location/Qualifiers
     source          1..3201
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q35"
     gene            1..3201
                     /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..165
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            166..202
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            203..1071
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     CDS             261..3125
                     /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_054859.2"
                     /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            1072..1122
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1123..1356
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1357..1407
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1408..1594
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1595..1745
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1746..1904
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1905..1970
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            1971..2111
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2112..2330
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2331..2401
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2402..2504
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2505..2687
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2688..2788
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2789..2885
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     exon            2886..3201
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3144..3149
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="hexamer: AATAAA"
     polyA_site      3165
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
     regulatory      3180..3185
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="hexamer: AATAAT"
     polyA_site      3201
                     /gene="SMARCAL1"
                     /gene_synonym="HARP; HHARP"
                     /note="major polyA site"
ORIGIN      
        1 agcccttcag gcctggccgc tacaataagg ctggcgaact cgcagcgctt gaatacccgt
       61 ggcctaaccg tccactcgga agaccggtcc cgctcgggag gctctgcagt cgcgcctggg
      121 gtcagggccg ggggcgaatg tggctcgcgt tctaggcctc cctgggttgg aaaaagacta
      181 tgttagcaag tgtcacgcca tgcttttgcc aactttccaa ttaaaggttg acattcctgc
      241 ataagcattt ctctgtgaaa atgtccttgc ctcttacaga ggagcagagg aaaaagattg
      301 aagagaatcg acaaaaggct ctggcccgca gagctgagaa gttattggca gaacagcatc
      361 agaggactag ctcgggcacc tccattgctg gcaacccatt ccaggccaag caaggcccat
      421 cccaaaattt cccaagggag tcttgtaagc cagtgagcca tggtgtcatt ttcaagcaac
      481 agaatctcag tagctcatct aatgctgacc aaagacctca tgattcccac agttttcagg
      541 caaagggaat atggaaaaag ccagaagaaa tgcccacagc ctgcccaggc cacagtccac
      601 gtagtcaaat ggctctcact ggaatctctc ctcccttggc acaaagtcct ccagaggtcc
      661 ctaaacaaca gctcttgagt tatgagttag gtcaaggtca tgctcaggct tcacctgaga
      721 tcaggttcac accctttgct aacccaactc ataagcctct ggccaaacca aagagttccc
      781 aagagacacc agctcattcc tctggacagc ctcccaggga tgctaagtta gaggccaaga
      841 cagcaaaagc ctccccttcg gggcagaaca tttcttacat ccattctagc tcagagagtg
      901 taacgcccag gacagaagga agactccagc agaagtcagg gtcctcagtc caaaaaggag
      961 tgaactctca gaagggaaag tgcgtaagga acggcgatcg tttccaggtg ttgattgggt
     1021 acaatgcgga actcattgca gtgtttaaga ccctgcccag caagaattat gatcctgaca
     1081 ccaagacgtg gaacttcagc atgaatgact atagtgccct gatgaaagca gcccagagcc
     1141 tccccacggt caacctgcag cctctggaat gggcctatgg cagcagcgag tcaccctcca
     1201 ccagcagtga gggacaggcc ggccttccat cagctccatc cctttcattt gtcaaagggc
     1261 gatgcatgct catctccagg gcctacttcg aggcagacat cagttattca caggacctta
     1321 ttgcgctttt taaacagatg gattccagaa gatatgatgt caagaccagg aagtggagct
     1381 ttctcttgga agagcacagt aaactaattg caaaggtgcg ctgcctccca caagttcagc
     1441 tggaccctct gcccacgact ctcaccctgg cgtttgcttc tcagctcaag aagacatctc
     1501 tcagtctcac gccagatgtc ccagaggcag acctttctga agtggacccc aagctcgtgt
     1561 ctaatctgat gccctttcag agagctggag tcaattttgc catagccaaa ggaggccgcc
     1621 tgctgctcgc tgacgacatg ggcctgggga agaccatcca agccatctgc atcgcagcct
     1681 tttaccggaa ggagtggccg ctcctggtgg tggtgccatc ctccgtgcgc ttcacctggg
     1741 agcaggcctt ccttcggtgg ctgccatctc tgagcccaga ttgcatcaac gtcgtggtga
     1801 ctgggaagga ccgcctgaca gctggcctga tcaacattgt cagctttgac cttcttagca
     1861 agttggaaaa acagctaaaa acccctttta aagttgtcat cattgatgaa tctcacttcc
     1921 tcaaaaacag taggactgcc cgctgtcgag cagctatgcc ggtcctaaag gttgccaaga
     1981 gggtgatcct gttgtcgggc acaccagcca tgtcccggcc cgcagagctc tacacgcaga
     2041 tcatcgcagt caagccaact ttcttccccc agtttcatgc ctttggactt cgctactgtg
     2101 atgccaaacg gatgccttgg gggtgggact actcaggttc ctccaacctg ggagagctga
     2161 agctcctgct ggaggaagca gtcatgctgc ggcgcctcaa gtccgacgtc ctttcccagc
     2221 tgcctgccaa gcagcgcaag atagtggtga ttgccccagg acggatcaat gccaggacca
     2281 gagctgccct ggatgctgca gccaaggaaa tgaccaccaa ggacaaaact aaacagcagc
     2341 agaaagatgc cctcattctc ttcttcaaca gaacagctga agctaaaatc ccatctgtca
     2401 ttgaatatat cttggaccta ctggaaagtg gaagagagaa gtttttagta tttgcacacc
     2461 ataaggtggt cctggacgca attacgcaag agcttgagag aaagcacgtg cagcacatcc
     2521 gcatcgatgg ctccacctca tcagctgagc gggaggacct gtgccagcag ttccaactgt
     2581 cggagaggca tgctgtggcc gtgctgtcca tcaccgctgc caatatgggc ctcaccttct
     2641 cctcggctga cctggtggtg tttgctgagc tgttttggaa cccaggggtg ctgatccagg
     2701 ctgaggaccg cgtgcaccgc attggacaga ccagctccgt gggcattcac tacctcgtgg
     2761 caaagggcac agctgatgac tacctttggc ccctgattca agagaagatt aaagttctgg
     2821 cagaagccgg gctttctgag accaattttt cagaaatgac agaatccact gattacctct
     2881 acaaggaccc aaagcagcag aagatctacg acctattcca gaagtccttt gagaaagaag
     2941 gaagtgatat ggagctcctg gaagcagcag agtcctttga cccaggaagt gcttcaggaa
     3001 catctggaag tagttcccag aacatgggag acaccctgga tgaaagctca ttgacagcca
     3061 gtccacagaa gaaaaggaga tttgaatttt ttgataactg ggacagcttt acgtctcccc
     3121 tgtaaaaggg gcaaaaagaa aaaaataaaa agcattttaa aatcatggaa ttgaaataaa
     3181 ataatgtatt ttgttttaaa a
//
