LOCUS       NM_001172509            5568 bp    mRNA    linear   PRI 29-OCT-2024
DEFINITION  Homo sapiens SATB homeobox 2 (SATB2), transcript variant 1, mRNA.
ACCESSION   NM_001172509
VERSION     NM_001172509.2
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 5568)
  AUTHORS   den Hoed,J., Hashimoto,H., Khan,M., Semmekrot,F., Bosanko,K.A.,
            Abe-Hatano,C., Nakagawa,E., Venselaar,H., Quercia,N., Chad,L.,
            Kurosaka,H., Rondeau,S., Fisher,S.E., Yamamoto,S. and Zarate,Y.A.
  TITLE     Pathogenic SATB2 missense variants affecting p.Gly392 have variable
            functional implications and result in diverse clinical phenotypes
  JOURNAL   J Med Genet 61 (11), 1062-1067 (2024)
   PUBMED   39327041
  REMARK    GeneRIF: Pathogenic SATB2 missense variants affecting p.Gly392 have
            variable functional implications and result in diverse clinical
            phenotypes.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5568)
  AUTHORS   Lee,J.A., Park,H.E., Jin,H.Y., Jin,L., Cho,N.Y., Bae,J.M., Kim,J.H.
            and Kang,G.H.
  TITLE     Concomitant expression patterns of CDX2 and SATB2 as prognostic
            factors in stage III colorectal cancers
  JOURNAL   Ann Diagn Pathol 71, 152289 (2024)
   PUBMED   38555678
  REMARK    GeneRIF: Concomitant expression patterns of CDX2 and SATB2 as
            prognostic factors in stage III colorectal cancers.
REFERENCE   3  (bases 1 to 5568)
  AUTHORS   Wahl,N., Espeso-Gil,S., Chietera,P., Nagel,A., Laighneach,A.,
            Morris,D.W., Rajarajan,P., Akbarian,S., Dechant,G. and
            Apostolova,G.
  TITLE     SATB2 organizes the 3D genome architecture of cognition in cortical
            neurons
  JOURNAL   Mol Cell 84 (4), 621-639 (2024)
   PUBMED   38244545
  REMARK    GeneRIF: SATB2 organizes the 3D genome architecture of cognition in
            cortical neurons.
REFERENCE   4  (bases 1 to 5568)
  AUTHORS   Wang,Z., She,D., Liu,L., Hua,X., Zhu,H., Yu,L., Wang,H., Zhu,Y.,
            Fan,G., Wang,Y., Xu,M. and Zhou,G.
  TITLE     Circular RNA CircSATB2 facilitates osteosarcoma progression through
            regulating the miR-661/FUS-mediated mRNA of ZNFX1
  JOURNAL   Cell Signal 114, 110977 (2024)
   PUBMED   37984605
  REMARK    GeneRIF: Circular RNA CircSATB2 facilitates osteosarcoma
            progression through regulating the miR-661/FUS-mediated mRNA of
            ZNFX1.
REFERENCE   5  (bases 1 to 5568)
  AUTHORS   Zhang,W., Wang,J., Huang,D., Liu,Z., Lu,T., Cui,C. and Li,Z.
  TITLE     Single-cell sequencing reveals SATB2/NOTCH1 signaling promotes the
            progression of malignancy of epithelial cells from papillary
            thyroid cancer
  JOURNAL   Mol Carcinog 63 (1), 22-33 (2024)
   PUBMED   37877736
  REMARK    GeneRIF: Single-cell sequencing reveals SATB2/NOTCH1 signaling
            promotes the progression of malignancy of epithelial cells from
            papillary thyroid cancer.
REFERENCE   6  (bases 1 to 5568)
  AUTHORS   Beaty,T.H., Hetmanski,J.B., Fallin,M.D., Park,J.W., Sull,J.W.,
            McIntosh,I., Liang,K.Y., Vanderkolk,C.A., Redett,R.J.,
            Boyadjiev,S.A., Jabs,E.W., Chong,S.S., Cheah,F.S., Wu-Chou,Y.H.,
            Chen,P.K., Chiu,Y.F., Yeow,V., Ng,I.S., Cheng,J., Huang,S., Ye,X.,
            Wang,H., Ingersoll,R. and Scott,A.F.
  TITLE     Analysis of candidate genes on chromosome 2 in oral cleft
            case-parent trios from three populations
  JOURNAL   Hum Genet 120 (4), 501-518 (2006)
   PUBMED   16953426
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 5568)
  AUTHORS   Vieira,A.R., Avila,J.R., Daack-Hirsch,S., Dragan,E., Felix,T.M.,
            Rahimov,F., Harrington,J., Schultz,R.R., Watanabe,Y., Johnson,M.,
            Fang,J., O'Brien,S.E., Orioli,I.M., Castilla,E.E.,
            Fitzpatrick,D.R., Jiang,R., Marazita,M.L. and Murray,J.C.
  TITLE     Medical sequencing of candidate genes for nonsyndromic cleft lip
            and palate
  JOURNAL   PLoS Genet 1 (6), e64 (2005)
   PUBMED   16327884
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 5568)
  AUTHORS   Dobreva,G., Dambacher,J. and Grosschedl,R.
  TITLE     SUMO modification of a novel MAR-binding protein, SATB2, modulates
            immunoglobulin mu gene expression
  JOURNAL   Genes Dev 17 (24), 3048-3061 (2003)
   PUBMED   14701874
REFERENCE   9  (bases 1 to 5568)
  AUTHORS   FitzPatrick,D.R., Carr,I.M., McLaren,L., Leek,J.P., Wightman,P.,
            Williamson,K., Gautier,P., McGill,N., Hayward,C., Firth,H.,
            Markham,A.F., Fantes,J.A. and Bonthron,D.T.
  TITLE     Identification of SATB2 as the cleft palate gene on 2q32-q33
  JOURNAL   Hum Mol Genet 12 (19), 2491-2501 (2003)
   PUBMED   12915443
  REMARK    GeneRIF: SATB2 is identified as the cleft palate gene on chromosome
            pair 2 which undergoes translocation.
REFERENCE   10 (bases 1 to 5568)
  AUTHORS   Zarate,Y.A., Bosanko,K. and Fish,J.
  TITLE     SATB2-Associated Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   29023086
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK056638.1 and AC016746.8.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_001172509.1.
            
            Summary: This gene encodes a DNA binding protein that specifically
            binds nuclear matrix attachment regions. The encoded protein is
            involved in transcription regulation and chromatin remodeling.
            Defects in this gene are associated with isolated cleft palate and
            cognitive disability. Alternate splicing results in multiple
            transcript variants that encode the same protein. [provided by
            RefSeq, Feb 2010].
            
            Transcript Variant: This variant (1) represents the longest
            transcript. Variants 1, 2 and 3 encode the same protein.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on 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 :: SRR14038194.2735146.1,
                                           SRR14038191.1650767.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000417098.6/ ENSP00000401112.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1314              AK056638.1         159-1472
            1315-1315           AC016746.8         136075-136075       c
            1316-3212           AK056638.1         1474-3370
            3213-5568           AC016746.8         36930-39285         c
FEATURES             Location/Qualifiers
     source          1..5568
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q33.1"
     gene            1..5568
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /note="SATB homeobox 2"
                     /db_xref="GeneID:23314"
                     /db_xref="HGNC:HGNC:21637"
                     /db_xref="MIM:608148"
     exon            1..601
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            602..829
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     CDS             661..2862
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /note="SATB family member 2; special AT-rich
                     sequence-binding protein 2; SATB2 fusion"
                     /codon_start=1
                     /product="DNA-binding protein SATB2"
                     /protein_id="NP_001165980.1"
                     /db_xref="CCDS:CCDS2327.1"
                     /db_xref="GeneID:23314"
                     /db_xref="HGNC:HGNC:21637"
                     /db_xref="MIM:608148"
                     /translation="MERRSESPCLRDSPDRRSGSPDVKGPPPVKVARLEQNGSPMGAR
                     GRPNGAVAKAVGGLMIPVFCVVEQLDGSLEYDNREEHAEFVLVRKDVLFSQLVETALL
                     ALGYSHSSAAQAQGIIKLGRWNPLPLSYVTDAPDATVADMLQDVYHVVTLKIQLQSCS
                     KLEDLPAEQWNHATVRNALKELLKEMNQSTLAKECPLSQSMISSIVNSTYYANVSATK
                     CQEFGRWYKKYKKIKVERVERENLSDYCVLGQRPMHLPNMNQLASLGKTNEQSPHSQI
                     HHSTPIRNQVPALQPIMSPGLLSPQLSPQLVRQQIAMAHLINQQIAVSRLLAHQHPQA
                     INQQFLNHPPIPRAVKPEPTNSSVEVSPDIYQQVRDELKRASVSQAVFARVAFNRTQG
                     LLSEILRKEEDPRTASQSLLVNLRAMQNFLNLPEVERDRIYQDERERSMNPNVSMVSS
                     ASSSPSSSRTPQAKTSTPTTDLPIKVDGANINITAAIYDEIQQEMKRAKVSQALFAKV
                     AANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQHERDVIYEEESRHHHSE
                     RMQHVVQLPPEPVQVLHRQQSQPAKESSPPREEAPPPPPPTEDSCAKKPRSRTKISLE
                     ALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHHGKLKEHLGS
                     AVDVAEYKDEELLTESEENDSEEGSEEMYKVEAEEENADKSKAAPAEIDQR"
     exon            830..1006
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            1007..1133
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            1134..1257
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            1258..1360
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            1361..1833
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            1834..2046
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            2047..2202
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            2203..2400
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     exon            2401..5568
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5550..5555
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /note="hexamer: AATAAA"
     polyA_site      5568
                     /gene="SATB2"
                     /gene_synonym="C2DELq32q33; DEL2Q32Q33; GLSS"
                     /note="major polyA site"
ORIGIN      
        1 gagtccggct ctggctgctg gcagaggcgg ccgagagggg agaggctgga ggtgacagct
       61 tgggcggccg ccgcgtttcc tcccgcgcgc ggtcccgggt ccctgcgtct tctcggctct
      121 tggtgttacc ggtcccaccg ctctggccgc gcctcctcgc gagctagccg ccctgcgaac
      181 cagcagcccc ggctcgccgc cgccgccgcc gcctccgggt tctcagccct ttctctccag
      241 aacgggtctc cttcccgaag gtgtgaaaag gctctttcag cctccttctc ttcccccctc
      301 ctccgccgtc ccctcccccg ctcgctcggg tgtccctttg gaggagtcct ttccctctcc
      361 tcctcctccc cctcctccct ccccccatca tcatcataac aaccatctcc gcaccagaag
      421 aagacaccct gacccaggac cttaaacatt aggacctggg gaagagggaa ggggaaggag
      481 taaagaggaa gactaggaga acactgcaaa gccaagcacc agaaactttc caccctggat
      541 tctctacttt tgctccatgg acagagcccc agtcagccaa gtttcagaca gaccgtgagc
      601 agtccctgtg cgttttattg cgacctgccg gtgggaactt tgtctccgag tcggagcagc
      661 atggagcggc ggagcgagag cccgtgtctg cgggacagcc ccgaccggcg gagcggcagc
      721 ccggacgtca aggggcctcc cccagtgaag gtggcccggc tggagcagaa cggcagcccc
      781 atgggagccc gcgggaggcc caacggcgcc gtggccaagg ccgtgggagg tttgatgatt
      841 cctgtctttt gtgtcgtgga gcagttggac ggctctcttg aatatgacaa cagagaagaa
      901 cacgccgagt ttgtcctggt gcggaaagat gtgcttttta gccagctggt ggagactgcg
      961 ctcctggccc tggggtattc tcacagctct gcggcccagg cccaaggaat aatcaagctg
     1021 ggaaggtgga accctctccc cctcagttat gtgacagatg cacccgacgc gacagtggcc
     1081 gacatgctac aagatgtcta tcatgttgtg acgttgaaaa tccaattaca aagttgttca
     1141 aagttggaag acttgcctgc ggagcagtgg aaccatgcca cagtccgcaa tgccttaaag
     1201 gaactgctca aagagatgaa ccagagcaca ttagccaaag aatgccctct ctcccagagt
     1261 atgatttcat ccattgtaaa tagcacatat tatgccaatg tgtcagcaac caagtgccag
     1321 gagtttggga gatggtataa aaagtacaag aagattaaag tggaaagagt ggaacgagaa
     1381 aacctttcag actattgtgt tctgggccag cgtccaatgc atttaccaaa tatgaaccag
     1441 ctggcatccc tggggaaaac caacgaacag tctcctcaca gccaaattca ccacagtact
     1501 ccaatccgaa accaagtgcc cgcattacag cccatcatga gccctggtct tctttctccc
     1561 cagcttagtc cacaacttgt aaggcaacaa atagccatgg cccatctgat aaaccaacag
     1621 attgccgtta gccggctcct ggctcaccag catcctcaag ccatcaacca gcagttcctg
     1681 aaccatccac ccatccccag agcagttaag ccagagccaa ccaactcttc cgtggaagtc
     1741 tctccagata tctaccagca agtcagagat gagctgaaga gggccagtgt gtcccaagct
     1801 gtctttgcaa gagtggcatt caaccgcaca cagggattgt tgtctgagat tctgcgtaag
     1861 gaagaagacc ctcggacagc ctctcagtct cttctagtaa acctgagggc catgcagaat
     1921 ttcctcaatc tgccagaagt ggagcgagat cgcatctacc aggatgagag ggagcggagc
     1981 atgaatccca atgtgagcat ggtctcctcg gcctccagca gtcccagctc ctcccgaacc
     2041 cctcaggcca aaacctcgac accgacaaca gacctcccta ttaaggtgga cggcgccaac
     2101 atcaacatca cagctgccat ttatgacgag atccaacagg agatgaaaag ggccaaggtg
     2161 tctcaagccc tgtttgccaa agtggctgca aataaaagtc agggctggct gtgtgaactg
     2221 ctccgctgga aggagaaccc aagcccagaa aaccgcaccc tctgggaaaa cctctgtacc
     2281 atccgtcgct tcctgaacct tccccagcat gagagggatg tcatctatga ggaggagtca
     2341 aggcatcacc acagcgaacg catgcaacac gtggtccagc ttccccctga gccggtgcag
     2401 gtacttcata gacagcagtc tcagccagcc aaggagagtt cccctcccag agaagaagcg
     2461 cctcccccac ctcctccgac tgaagacagt tgtgccaaaa agccccggtc tcgcacaaag
     2521 atctccttag aagccctggg gatcctccaa agctttattc atgatgtagg cctgtaccca
     2581 gaccaggaag ccatccacac tctttcggct cagctggatc tccccaaaca caccatcatc
     2641 aagttcttcc agaaccagcg gtaccacgtg aagcaccacg ggaagctgaa agagcacctg
     2701 ggctccgcgg tggacgtggc tgaatataag gacgaggagc tgctgaccga gtcagaggag
     2761 aacgacagcg aggaaggctc cgaggagatg tacaaagtgg aggctgagga ggaaaatgct
     2821 gacaaaagca aggcagcacc tgccgaaatt gaccagagat aatgtgaact tctactaggc
     2881 aaagcaatac atcggtccaa ggattttctg ctttcatttc tttaaaagtt ttttgttagt
     2941 ttgttttttg tttttgtttt tgggtttttt tggctttatt tttgtctttt tatgtctgtt
     3001 ttgtttttct tacccttttg gacatttctt tgttgcacag gatacaccta tagactgaat
     3061 aagttcagta tttccgaatc agacatcgcc ttggcaaaga cactaaagcg ttacacttta
     3121 tcccgtctct atgactggat catagtcatt ataatcacag gagactctgc cttcattatc
     3181 cttgcactta acggaagtta catcaggcaa gtaccaggat gaaaagaact atgaaataaa
     3241 tgaaggaagc tacaagtgtg tgtgtatatg tatatgtata tatctctata tttacatata
     3301 tatattaaaa ttgcatggga cagagacttt gcaatccgaa agaatagact gtgaaatgag
     3361 ttcttaaaga aaagacttgt ttatgtatta aaaaaaccac ttcacagtga gtcgctttgg
     3421 ctttttgata aactgcggcc tgctctcagg gtggggtgac tatttttgaa ttcctattta
     3481 ttttttgtgt ttgtccctga tttttttttt ttaattctat ggcttcctat ctggcagctt
     3541 aatgggtaat ttttgaggta tgtatttaac aaaataaacg acactgccga aaaaaaaaaa
     3601 agtgaagtga aaacaatcag ggcacattaa aatgatacaa gtcaaataaa tcttaaagac
     3661 acaatgcaca cttaaaatga ctcaataaaa tgacttgcta cgttccgtta ttcaatttgt
     3721 cattactgta gtgaacagat gcatttctgt ggaattccaa ataagtaaaa ctgaaattca
     3781 gtgcagagaa aactttgtcc actagtgcaa gtcttgatca aatgacattt tgacattgga
     3841 catatggaat tcatagtatg agccacattt tgttgtgaaa tttatttacc tgcttgtggc
     3901 ttcaaatctg aaaattaata agcctgctcg tttaaaagtt gtttgttgtt gctgtttttt
     3961 tgtctttttg ttttttacta gaaaatagtt cagtgtaata ttaagttaga aaagaagttg
     4021 ctgcccagtt aaaggggctc cctctcaaat aaatctccat ccttccctct cccaaaagac
     4081 atttctgatt tctgcttcac tttgggcttc ctcttcttcg tacacattcc atctacctaa
     4141 tcaaacattt tcagtccctg atctctcctg tcccttttcc tgggatgaca gccctaacaa
     4201 gaactgtttt tgaatcgttg tgcagctcca ggcaatagag tatgtgaagc gatttcagta
     4261 gaatcactta ctcatcctaa aagaaaacat tatcccagtt acctacatcg caattacctt
     4321 atgtaaagca gaactaatgc tgactggatg tttaatggga tgagcattaa agctgcaatc
     4381 tactatagta ctccagatct ctttcggctt cctatgagaa acaccagaag cattactttc
     4441 cacttctact tacagtaatt gcaagaggag acctcacatt caggactggc ctagtgaacg
     4501 taatccatgc tttaaactgg ccattaaaca gtcccacatg gttggatttt tttttttttt
     4561 ttgagttgtg ctttcacaaa accttgtcaa agacctcatg caatatcact ttgaaagtta
     4621 ttttctgttt actacacaaa cattgtaata taactgttaa tactatttat atatttgaaa
     4681 ggtataaaag gtaggagtta aaaaaaaaac ctctatgtgt agatattaac tcagaactta
     4741 caatatacag ggagaagaca tgttgcaata caagctaatt ctagctgctc agtaacctct
     4801 ggagttttta aagggacatt ttcctgtact ttttcaaata atgatgttta aaaattatct
     4861 tgacataagc gtcatatacc tttgcaaaag gatggttgtt tgcagttagc cctggcccca
     4921 tccttcctat ttctgtagta tgctgcagct ttaatcagaa agtccatggt tgctgcttcc
     4981 tgatctccga gttactcttt ccaaattgtc ttcttacact gttgctgaag gtcactctgt
     5041 acacgtaatg gaaactgatt ttgccaagct cttacaaggt ggttcatcta tcgatggcat
     5101 ccgcatttgg tatcttttac acttcaacca aaaatttatt aggtattttt caatgctaag
     5161 tcttgccttt tattttttaa tttcactgcc aagtttgcag tggttctaag tgaatctgtg
     5221 ggcattttag cctgtggtct tgccagatct ttgcgaatta caatgcatat atgtctattt
     5281 attcaatatc tgtcatataa tatctatttg gaagaagaaa ctttctcttg tagtgcctct
     5341 tgacaaagca caatttcccg cctttttttt tttttgtgaa atgaaaaaaa caaattgtgt
     5401 tttattgcgg tatcaacaat gtgaataagg attaacatat tgtaaatgtt cttttttcca
     5461 tgtaaatcaa ctatctttgt tatcactaag tgataattaa tttttaactt atgtgcattg
     5521 ttaggctgtt agaatttttt ggttgttaaa ataaacgcat tcaataaa
//
