LOCUS       NM_002968               5134 bp    mRNA    linear   PRI 12-OCT-2024
DEFINITION  Homo sapiens spalt like transcription factor 1 (SALL1), transcript
            variant 1, mRNA.
ACCESSION   NM_002968
VERSION     NM_002968.3
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 5134)
  AUTHORS   Chi,Y., Yao,Y., Sun,F., Zhang,W., Zhang,Z., Wang,Y. and Hao,W.
  TITLE     A novel SALL1 C757T mutation in a Chinese family causes a rare
            disease --Townes-Brocks syndrome
  JOURNAL   Ital J Pediatr 50 (1), 121 (2024)
   PUBMED   38915054
  REMARK    GeneRIF: A novel SALL1 C757T mutation in a Chinese family causes a
            rare disease --Townes-Brocks syndrome.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5134)
  AUTHORS   Innoceta,A.M., Olivucci,G., Parmeggiani,G., Scarano,E.,
            Pragliola,A. and Graziano,C.
  TITLE     Chromosomal Microarray Analysis Identifies a Novel SALL1 Deletion,
            Supporting the Association of Haploinsufficiency with a Mild
            Phenotype of Townes-Brocks Syndrome
  JOURNAL   Genes (Basel) 14 (2), 258 (2023)
   PUBMED   36833185
  REMARK    GeneRIF: Chromosomal Microarray Analysis Identifies a Novel SALL1
            Deletion, Supporting the Association of Haploinsufficiency with a
            Mild Phenotype of Townes-Brocks Syndrome.
            Review article
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 5134)
  AUTHORS   Lugli,L., Rossi,C., Ceccarelli,P.L., Calabrese,O., Bedetti,L.,
            Miselli,F., Bianchini,M.A., Iughetti,L. and Berardi,A.
  TITLE     Townes-Brocks syndrome with craniosynostosis in two siblings
  JOURNAL   Eur J Med Genet 65 (12), 104642 (2022)
   PUBMED   36252910
  REMARK    GeneRIF: Townes-Brocks syndrome with craniosynostosis in two
            siblings.
REFERENCE   4  (bases 1 to 5134)
  AUTHORS   Qian,C., Yang,Y., Lan,T., Wang,Y. and Yao,J.
  TITLE     Hsa_circ_0043265 Restrains Cell Proliferation, Migration and
            Invasion of Tongue Squamous Cell Carcinoma via Targeting the
            miR-1243/SALL1 Axis
  JOURNAL   Pathol Oncol Res 27, 587130 (2021)
   PUBMED   34257535
  REMARK    GeneRIF: Hsa_circ_0043265 Restrains Cell Proliferation, Migration
            and Invasion of Tongue Squamous Cell Carcinoma via Targeting the
            miR-1243/SALL1 Axis.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 5134)
  AUTHORS   Forghanifard,M.M., Kasebi,P. and Abbaszadegan,M.R.
  TITLE     SOX2/SALL4 stemness axis modulates Notch signaling genes to
            maintain self-renewal capacity of esophageal squamous cell
            carcinoma
  JOURNAL   Mol Cell Biochem 476 (2), 921-929 (2021)
   PUBMED   33098486
  REMARK    GeneRIF: SOX2/SALL4 stemness axis modulates Notch signaling genes
            to maintain self-renewal capacity of esophageal squamous cell
            carcinoma.
REFERENCE   6  (bases 1 to 5134)
  AUTHORS   Kohlhase,J., Taschner,P.E., Burfeind,P., Pasche,B., Newman,B.,
            Blanck,C., Breuning,M.H., ten Kate,L.P., Maaswinkel-Mooy,P.,
            Mitulla,B., Seidel,J., Kirkpatrick,S.J., Pauli,R.M.,
            Wargowski,D.S., Devriendt,K., Proesmans,W., Gabrielli,O.,
            Coppa,G.V., Wesby-van Swaay,E., Trembath,R.C., Schinzel,A.A.,
            Reardon,W., Seemanova,E. and Engel,W.
  TITLE     Molecular analysis of SALL1 mutations in Townes-Brocks syndrome
  JOURNAL   Am J Hum Genet 64 (2), 435-445 (1999)
   PUBMED   9973281
REFERENCE   7  (bases 1 to 5134)
  AUTHORS   Marlin,S., Blanchard,S., Slim,R., Lacombe,D., Denoyelle,F.,
            Alessandri,J.L., Calzolari,E., Drouin-Garraud,V., Ferraz,F.G.,
            Fourmaintraux,A., Philip,N., Toublanc,J.E. and Petit,C.
  TITLE     Townes-Brocks syndrome: detection of a SALL1 mutation hot spot and
            evidence for a position effect in one patient
  JOURNAL   Hum Mutat 14 (5), 377-386 (1999)
   PUBMED   10533063
REFERENCE   8  (bases 1 to 5134)
  AUTHORS   Kohlhase,J., Wischermann,A., Reichenbach,H., Froster,U. and
            Engel,W.
  TITLE     Mutations in the SALL1 putative transcription factor gene cause
            Townes-Brocks syndrome
  JOURNAL   Nat Genet 18 (1), 81-83 (1998)
   PUBMED   9425907
REFERENCE   9  (bases 1 to 5134)
  AUTHORS   Kohlhase,J., Schuh,R., Dowe,G., Kuhnlein,R.P., Jackle,H.,
            Schroeder,B., Schulz-Schaeffer,W., Kretzschmar,H.A., Kohler,A.,
            Muller,U., Raab-Vetter,M., Burkhardt,E., Engel,W. and Stick,R.
  TITLE     Isolation, characterization, and organ-specific expression of two
            novel human zinc finger genes related to the Drosophila gene spalt
  JOURNAL   Genomics 38 (3), 291-298 (1996)
   PUBMED   8975705
REFERENCE   10 (bases 1 to 5134)
  AUTHORS   Graziano,C. and Olivucci,G.
  TITLE     SALL1-Related Townes-Brocks Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301618
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BP229682.1, DA318592.1 and
            AC009166.4.
            
            On Aug 31, 2019 this sequence version replaced NM_002968.2.
            
            Summary: The protein encoded by this gene is a zinc finger
            transcriptional repressor and may be part of the NuRD histone
            deacetylase complex (HDAC). Defects in this gene are a cause of
            Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome
            (BOR). Two transcript variants encoding different isoforms have
            been found for this gene. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (a).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments.
            
            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 :: SRR14038192.1308398.1, EU668343.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968189, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000251020.9/ ENSP00000251020.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-26                BP229682.1         4-29
            27-591              DA318592.1         1-565
            592-3563            AC009166.4         90502-93473
            3564-5134           AC009166.4         94609-96179
FEATURES             Location/Qualifiers
     source          1..5134
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q12.1"
     gene            1..5134
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /note="spalt like transcription factor 1"
                     /db_xref="GeneID:6299"
                     /db_xref="HGNC:HGNC:10524"
                     /db_xref="MIM:602218"
     exon            1..105
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /inference="alignment:Splign:2.1.0"
     CDS             30..4004
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /note="isoform a is encoded by transcript variant 1;
                     sal-like protein 1; zinc finger protein SALL1; zinc finger
                     protein 794; zinc finger protein Spalt-1; epididymis
                     secretory protein Li 89"
                     /codon_start=1
                     /product="sal-like protein 1 isoform a"
                     /protein_id="NP_002959.2"
                     /db_xref="CCDS:CCDS10747.1"
                     /db_xref="GeneID:6299"
                     /db_xref="HGNC:HGNC:10524"
                     /db_xref="MIM:602218"
                     /translation="MSRRKQAKPQHFQSDPEVASLPRRDGDTEKGQPSRPTKSKDAHV
                     CGRCCAEFFELSDLLLHKKNCTKNQLVLIVNENPASPPETFSPSPPPDNPDEQMNDTV
                     NKTDQVDCSDLSEHNGLDREESMEVEAPVANKSGSGTSSGSHSSTAPSSSSSSSSSSG
                     GGGSSSTGTSAITTSLPQLGDLTTLGNFSVINSNVIIENLQSTKVAVAQFSQEARCGG
                     ASGGKLAVPALMEQLLALQQQQIHQLQLIEQIRHQILLLASQNADLPTSSSPSQGTLR
                     TSANPLSTLSSHLSQQLAAAAGLAQSLASQSASISGVKQLPPIQLPQSSSGNTIIPSN
                     SGSSPNMNILAAAVTTPSSEKVASSAGASHVSNPAVSSSSSPAFAISSLLSPASNPLL
                     PQQASANSVFPSPLPNIGTTAEDLNSLSALAQQRKSKPPNVTAFEAKSTSDEAFFKHK
                     CRFCAKVFGSDSALQIHLRSHTGERPFKCNICGNRFSTKGNLKVHFQRHKEKYPHIQM
                     NPYPVPEHLDNIPTSTGIPYGMSIPPEKPVTSWLDTKPVLPTLTTSVGLPLPPTLPSL
                     IPFIKTEEPAPIPISHSATSPPGSVKSDSGGPESATRNLGGLPEEAEGSTLPPSGGKS
                     EESGMVTNSVPTASSSVLSSPAADCGPAGSATTFTNPLLPLMSEQFKAKFPFGGLLDS
                     AQASETSKLQQLVENIDKKATDPNECIICHRVLSCQSALKMHYRTHTGERPFKCKICG
                     RAFTTKGNLKTHYSVHRAMPPLRVQHSCPICQKKFTNAVVLQQHIRMHMGGQIPNTPV
                     PDSYSESMESDTGSFDEKNFDDLDNFSDENMEDCPEGSIPDTPKSADASQDSLSSSPL
                     PLEMSSIAALENQMKMINAGLAEQLQASLKSVENGSIEGDVLTNDSSSVGGDMESQSA
                     GSPAISESTSSMQALSPSNSTQEFHKSPSIEEKPQRAVPSEFANGLSPTPVNGGALDL
                     TSSHAEKIIKEDSLGILFPFRDRGKFKNTACDICGKTFACQSALDIHYRSHTKERPFI
                     CTVCNRGFSTKGNLKQHMLTHQMRDLPSQLFEPSSNLGPNQNSAVIPANSLSSLIKTE
                     VNGFVHVSPQDSKDTPTSHVPSGPLSSSATSPVLLPALPRRTPKQHYCNTCGKTFSSS
                     SALQIHERTHTGEKPFACTICGRAFTTKGNLKVHMGTHMWNSTPARRGRRLSVDGPMT
                     FLGGNPVKFPEMFQKDLAARSGSGDPSSFWNQYAAALSNGLAMKANEISVIQNGGIPP
                     IPGSLGSGNSSPVSGLTGNLERLQNSEPNAPLAGLEKMASSENGTNFRFTRFVEDSKE
                     IVTS"
     exon            106..3563
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /inference="alignment:Splign:2.1.0"
     exon            3564..5134
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4416..4421
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /note="hexamer: AATAAA"
     polyA_site      4438
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /note="major polyA site"
     regulatory      5103..5108
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /note="hexamer: AATACA"
     polyA_site      5134
                     /gene="SALL1"
                     /gene_synonym="HEL-S-89; HSAL1; Sal-1; TBS; ZNF794"
                     /note="major polyA site"
ORIGIN      
        1 attctgcccc agctgatgtt tgagccagca tgtcgcggag gaagcaagcg aagcctcaac
       61 atttccaatc cgaccccgaa gtggcctcgc tcccccggcg agatggagac acagaaaagg
      121 gtcaaccgag tcgccctact aagagcaagg atgcccacgt ctgtggccgg tgctgtgccg
      181 agttctttga attatcagat cttctgctcc acaagaagaa ctgtactaaa aatcaattag
      241 ttttaatcgt aaatgaaaat ccagcctccc cacccgaaac cttctccccc agcccccctc
      301 ctgataatcc tgatgaacaa atgaatgaca cagttaacaa aacagatcaa gtggactgca
      361 gcgacctttc agaacacaac ggacttgaca gggaagagtc catggaggtg gaggccccgg
      421 ttgctaacaa aagcggcagc ggcacttcca gcggcagcca cagcagtacc gccccaagca
      481 gcagcagcag cagcagcagc agcagcggcg gcggcggcag ctcctccaca ggtacctcag
      541 cgatcacaac ctctctacct caactcgggg acctgacaac actgggcaac ttctccgtaa
      601 tcaacagcaa cgtcatcatc gagaacctcc agagcaccaa ggtggcggtg gcccagttct
      661 cccaggaagc gaggtgcggc ggggcctctg ggggcaagct ggccgtccca gccctcatgg
      721 aacaactcct agctctgcag cagcagcaga tccaccagct gcaattgatc gaacagattc
      781 gtcaccaaat attgctgttg gcttctcaga atgcagactt gccaacatct tctagtcctt
      841 ctcaaggtac tttacgaaca tctgccaacc ccttgtccac gctaagttcc catttatctc
      901 agcagctggc agcagcagct ggattggcac agagcctcgc cagccaatct gccagcatta
      961 gtggtgtgaa acagctaccc ccaatccagc tacctcagag cagttctggc aacaccatca
     1021 ttccatccaa cagcggctct tctcccaata tgaacatatt ggcagcggca gttaccaccc
     1081 cgtcctctga aaaagtggct tcaagtgctg gggcctccca tgtcagcaac ccagcggtct
     1141 catcatcgtc ctcaccagct tttgcaataa gcagtttatt aagtcctgcg tctaatccac
     1201 ttctacctca gcaagcctcc gctaactcgg ttttccccag ccctttgccc aacatcggaa
     1261 caactgcaga ggatttaaac tccttgtctg ccttggccca gcaaagaaaa agcaagccac
     1321 caaatgtcac tgcctttgaa gcgaaaagta cttccgatga ggcattcttc aaacacaagt
     1381 gcaggttctg cgcgaaggtc tttgggagtg acagtgcctt gcagatccac ttgcgttccc
     1441 ataccggaga gaggccattc aagtgcaaca tctgcgggaa caggttctcc accaagggga
     1501 atctgaaagt ccactttcag cgccacaaag agaaataccc tcatatccag atgaacccct
     1561 atcctgtgcc tgagcatttg gacaatatcc ccacgagtac tggcatccca tatggcatgt
     1621 ccatccctcc agagaagcca gtcaccagct ggctagacac caaaccagtc ctgcctactc
     1681 tgaccacttc agtcggcctg ccgttgcccc caaccctccc aagcctcata cccttcatca
     1741 agacggaaga gccagccccc atccccatca gccattctgc caccagcccc ccaggctcag
     1801 tcaaaagtga ctccgggggc cctgagtcag ccacaagaaa cctaggtggg ctcccagagg
     1861 aagccgaagg gtccactctg ccaccctctg gtggcaaaag cgaagagagt ggcatggtca
     1921 ccaactcagt cccgacggcg agcagtagcg tcctgagctc cccagcggca gactgcggcc
     1981 ccgcgggcag tgccaccacc ttcaccaacc ctttgttgcc gctcatgtcc gagcagttca
     2041 aggccaagtt tccttttggg ggactcctgg actcagctca ggcatcagag acgtccaagc
     2101 ttcagcaact ggtagaaaac attgacaaga aggccactga ccccaatgag tgcatcatct
     2161 gccaccgggt tctcagctgc cagagcgcct tgaaaatgca ctacaggaca cacactgggg
     2221 agaggccctt taagtgtaag atctgtggcc gggctttcac cacgaaaggg aatcttaaaa
     2281 cccactacag tgtccatcgt gctatgcccc cgctcagagt ccagcattcc tgccccatct
     2341 gccagaagaa gttcacgaac gctgtggtcc tgcagcagca catccgaatg catatgggag
     2401 gccagatccc caacacccca gtccccgaca gctactctga gtccatggag tctgacacag
     2461 gttcctttga tgagaaaaat tttgatgacc tagacaactt ctctgatgaa aacatggaag
     2521 actgtcctga gggcagcatc cctgatacac ctaagtctgc agacgcctcc caagacagct
     2581 tatcctcttc gcctttgccc ctcgagatgt cgagcatcgc tgctttggaa aatcagatga
     2641 agatgatcaa tgctggcctg gcagagcagc tacaggccag cctgaagtca gtggagaatg
     2701 ggtccatcga gggggatgtc ctgaccaatg attcatcctc agtgggtggt gacatggaaa
     2761 gccaaagtgc tggcagccca gccatctcag agtctacctc ttccatgcag gctctgtccc
     2821 cgtccaacag cacgcaggag ttccacaagt cacccagcat tgaggagaaa ccacagagag
     2881 cggtcccaag cgagtttgcc aatggtttgt ctcccacccc agtgaatggt ggggctttgg
     2941 atttgacatc tagtcacgca gagaaaatca tcaaagaaga ttctttgggg atcctcttcc
     3001 cttttagaga ccggggtaaa tttaaaaaca ctgcttgtga catttgtggc aaaacatttg
     3061 cttgtcagag tgccttggac attcactata gaagtcatac caaagagaga ccatttattt
     3121 gcacagtttg caatcgtggc ttttccacaa agggtaattt gaagcagcac atgttgacac
     3181 atcagatgcg agatctgcca tcccagctct ttgagcccag ttccaacctt ggccccaatc
     3241 agaactcagc ggtgattccc gccaactcgt tgtcatctct catcaagaca gaggtcaacg
     3301 gcttcgtgca tgtttctcct caggacagta aggacacccc caccagtcac gtcccgtctg
     3361 ggcctctgtc ttcctctgcc acatccccag ttctgctccc tgctctgccc aggagaactc
     3421 ccaagcagca ctactgcaac acatgtggca aaaccttctc ctcatcgagt gccctgcaga
     3481 ttcacgagag aactcacact ggagagaaac cctttgcttg cactatttgt ggaagagctt
     3541 tcacgactaa aggcaatctt aaggtacaca tgggcactca catgtggaat agcacccctg
     3601 cacgacgggg tcggcggctc tctgtggatg gccccatgac atttctagga ggcaatcccg
     3661 tcaagttccc agaaatgttc cagaaggatt tggcggcaag atcaggaagt ggggatcctt
     3721 ccagcttctg gaatcagtat gcagcagcgc tctccaacgg gctggcgatg aaggccaacg
     3781 agatctccgt cattcagaac ggtggcatcc ctccaattcc tggaagcctc ggcagtggga
     3841 acagctcacc tgttagtggg ctgacgggaa acctggagag gctccagaac tcagagccca
     3901 atgctcccct ggccggcctg gagaaaatgg caagcagtga gaacggaacc aacttccgct
     3961 tcacccgctt cgtggaggac agcaaggaga tcgtcacgag ttaaagcagc tcgggctgga
     4021 gacatagcat tcattcctgt tcagaatgcg acctatggtg gcctcctact ccttgccccc
     4081 caccccgccc cgccccttcc ttctgttccc cagatctatg aactacaaca ttatgaagac
     4141 attcttttgt accttgttca actttagagt tctaagaaag cttatttatt agcgatataa
     4201 ccttgctttg caaacagaat gcaagcgtta actttggtct tctgtatttt ggactaaata
     4261 ctaattgact agagtgctgt aaacttgctg taacatttat ggcaattgca agttgccctg
     4321 ctaggcagtt gtaatctggc attaacttat tttctatatc cagtttaata tgaatctggt
     4381 gttgatgcaa tgcctcagtg atgcattaga tctctaataa agtctgtata tacatgtaca
     4441 ctttgatcct gctggaaaat tttatcagca aacacattgt ctaatctttc aaaacagatt
     4501 taaggaaagg actgaaagta cagactgaac agtgtggttc tttgaaaggt ttggtttttt
     4561 aatttttatt ctaaaattca accttttttt ttgtcgattt aaccatttcc attttgaact
     4621 gctatttgta ttgtgctttt tacttgagtc gtcttcaatg ttaataagtt tctgtacagt
     4681 aataagcacg cagaattctt tagagaaaaa gaaaacaagc gttgttttgg tagttgaaac
     4741 tgagacgtaa cattttgcct tgtaggtata ttcacgatag aaaatgtgtg ctggaatttc
     4801 acaatgctgc taagtatagc atcttgaaca accttcagtg gagaaaatgt agatgctctt
     4861 gtatatacaa taagaaatat cactttcatt caaatgtaca tatgttcctt acaagagcaa
     4921 atgcttcttc ttgatcaaga gagcaggtat agtgtttgtt tattttgtct taggtatgga
     4981 agaaaaaaat tggactgtta catgcacttt cttggaaagt tgaaaggaaa gggggggtcc
     5041 aatttcttta acatttaata cttactaaca acagagatac tgtaatttta ctcaagtaat
     5101 caaatacatt ttttttgcaa cagataaaac aaaa
//
