LOCUS       AH011517                5310 bp    DNA     linear   HUM 10-JUN-2016
DEFINITION  Homo sapiens isolate Pima Indian Genomic DNA, #657 LIM homeobox
            transcription factor 1 (LMX1A) gene, complete cds, alternatively
            spliced; and LIM homeobox transcription factor 1 alpha variant 6A
            (LMX1A) gene, complete sequence.
ACCESSION   AH011517 AY078391 AY078392 AY078393 AY078394 AY078395 AY078396
            AY078397 AY078398
VERSION     AH011517.2
KEYWORDS    .
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 5310)
  AUTHORS   Thameem,F., Wolford,J.K., Wang,J., German,M.S., Bogardus,C. and
            Prochazka,M.
  TITLE     Cloning, expression and genomic structure of human LMX1A, and
            variant screening in Pima Indians
  JOURNAL   Gene 290 (1-2), 217-225 (2002)
   PUBMED   12062816
REFERENCE   2  (bases 1 to 5310)
  AUTHORS   Thameem,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-FEB-2002) Clinical Diabetes and Nutrition Section,
            NIDDK, NIH, 4212, North 16th Street, Phoenix, AZ 85016, USA
COMMENT     On or before Jun 10, 2016 this sequence version replaced
            AY078391.1, AY078392.1, AY078393.1, AY078394.1, AY078395.1,
            AY078396.1, AY078397.1, AY078398.1, AH011517.1.
FEATURES             Location/Qualifiers
     source          1..5310
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /isolate="Pima Indian Genomic DNA, #657"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q22"
     gene            <1..5305
                     /gene="LMX1A"
     regulatory      <1..133
                     /regulatory_class="promoter"
                     /gene="LMX1A"
     variation       50
                     /gene="LMX1A"
                     /replace="a"
     mRNA            join(134..430,1072..1258,1504..1736,1980..2152,3317..3394,
                     3661..3730,4539..4709,4953..5305)
                     /gene="LMX1A"
                     /product="LIM homeobox transcription factor 1 alpha"
                     /note="alternative transcript"
     exon            134..430
                     /gene="LMX1A"
                     /number=1
     5'UTR           134..354
                     /gene="LMX1A"
     CDS             join(355..430,1072..1258,1504..1736,1980..2152,3317..3394,
                     3661..3730,4539..4709,4953..5113)
                     /gene="LMX1A"
                     /note="alternatively spliced"
                     /codon_start=1
                     /product="LIM homeobox transcription factor 1 alpha"
                     /protein_id="AAL82892.1"
                     /translation="MLDGLKMEENFQSAIDTSASFSSLLGRAVSPKSVCEGCQRVILD
                     RFLLRLNDSFWHEQCVQCASCKEPLETTCFYRDKKLYCKYDYEKLFAVKCGGCFEAIA
                     PNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGDYEKERELLSLVSP
                     AASDSGKSDDEESLCKSAHGAGKGTAEEGKDHKRPKRPRTILTTQQRRAFKASFEVSS
                     KPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRQQQQQQDQQNTQRLSSAQTN
                     GGGSAGMEGIMNPYTALPTPQQLLAIEQSVYSSDPFRQGLTPPQMPGDHMHPYGAEPL
                     FHDLDSDDTSLSNLGDCFLATSEAGPLQSRVGNPIDHLYSMQNSYFTS"
     variation       856
                     /gene="LMX1A"
                     /replace="g"
     gap             901..1000
                     /estimated_length=unknown
     exon            1072..1258
                     /gene="LMX1A"
                     /number=2
     gap             1301..1400
                     /estimated_length=unknown
     exon            1504..1736
                     /gene="LMX1A"
                     /number=3
     variation       1589
                     /gene="LMX1A"
                     /replace="t"
     mRNA            join(1592..1736,1980..2152,3317..3394,3661..3730,
                     4179..4311,4539..4709,4953..5305)
                     /gene="LMX1A"
                     /product="LIM homeobox transcription factor 1 alpha
                     variant 6A"
                     /note="alternative transcript detected only in testis
                     cDNA; coding region not determined"
     misc_feature    1592
                     /gene="LMX1A"
                     /note="transcription start site for alternative transcript
                     encoding LMX1-6A"
     gap             1821..1920
                     /estimated_length=unknown
     exon            1980..2152
                     /gene="LMX1A"
                     /number=4
     mRNA            join(2516..2585,2738..2834,3317..3394,3661..3730,
                     4539..4709,4953..5305)
                     /gene="LMX1A"
                     /product="LIM homeobox transcription factor 1 alpha
                     variant 4AB"
                     /note="alternative transcript detected only in testis
                     cDNA"
     exon            2516..2585
                     /gene="LMX1A"
                     /note="alternative exon for LMX1-4AB; detected only in
                     testis cDNA"
                     /number=4a
     variation       2539
                     /gene="LMX1A"
                     /replace="a"
     variation       2675
                     /gene="LMX1A"
                     /replace="g"
     exon            2738..2834
                     /gene="LMX1A"
                     /note="alternative exon for LMX1-4AB; detected only in
                     testis cDNA"
                     /number=4b
     gap             2881..2980
                     /estimated_length=unknown
     variation       2992
                     /gene="LMX1A"
                     /replace="c"
     variation       3241
                     /gene="LMX1A"
                     /replace="t"
     exon            3317..3394
                     /gene="LMX1A"
                     /number=5
     gap             3461..3560
                     /estimated_length=unknown
     CDS             join(3661..3730,4539..4709,4953..5113)
                     /gene="LMX1A"
                     /note="LMX1-4AB; alternatively spliced"
                     /codon_start=1
                     /product="LIM homeobox transcription factor 1 alpha
                     variant 4AB"
                     /protein_id="AAL82893.1"
                     /translation="MKKLARRQQQQQQDQQNTQRLSSAQTNGGGSAGMEGIMNPYTAL
                     PTPQQLLAIEQSVYSSDPFRQGLTPPQMPGDHMHPYGAEPLFHDLDSDDTSLSNLGDC
                     FLATSEAGPLQSRVGNPIDHLYSMQNSYFTS"
     exon            3661..3730
                     /gene="LMX1A"
                     /number=6
     exon            4179..4311
                     /gene="LMX1A"
                     /note="alternative exon for LMX1-6A; detected only in
                     testis cDNA"
                     /number=6A
     gap             4401..4500
                     /estimated_length=unknown
     exon            4539..4709
                     /gene="LMX1A"
                     /number=7
     gap             4801..4900
                     /estimated_length=unknown
     exon            4953..5305
                     /gene="LMX1A"
                     /number=8
BASE COUNT         1060 a         1179 c         1228 g         1143 t
ORIGIN      
        1 gtataggttg gggcggagtc ggattcggga tggaaaacct ggggcaaggg atgtaggtgg
       61 gggtgagggg ggcaggagaa ggagaaacgc agttgggggg cggaggccta agtacataac
      121 gtgttgactt caagtgaaat cagatcagcc agagcagttc gctgtgactg atctctcctc
      181 ccaccctaca ttctcttggc tggaccctat cctcctggct gattctggtc gccctggaca
      241 ctccctcagt tctttcccag gagtgcggtg gctgctggcg ccgagtccca gcgggcacgg
      301 acgtcagacg catcgtttct tctcctctac aggtcctccc ggcccggccc gaacatgctg
      361 gacggcctaa agatggagga gaacttccaa agcgcgatcg acacctcggc ctccttctcc
      421 tcgctgctgg gtgagtgttc aggccgtgcg tcctgggcgc actctctttc cgcttggcgc
      481 tgagctctgg agccccgctc tctgggacct ggtccgcgat agggaagcta gcgcccctct
      541 tcatacacta aattgagccc catcactatc tgtccgtcag tgcttgtggg tcgtccctac
      601 ccaaataaat ccaacaagcc gccccaggcc tcacgcactg ggcaccgaat tccccaaagc
      661 cgcgaggggc gggcgagctt gttcgtaggc gtctgagtgg caagtgatta aaaataccca
      721 gggctggatt tttaatctcg gagctgatcg acgtctcata aatgccgccc tcttctcgcg
      781 gcctagaggc aatagcatcc gagacccgag gcctggagcg cccaagttcg aggaggcttc
      841 tctcccccac caactccagc cccaatttca gccatgggca aggccgagag agacttttct
      901 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
      961 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn gggtcccggc caggtttggc
     1021 atggtctacc tgcccgggct gctcacccgc caacgtctgt tgtggctaca ggcagagcgg
     1081 tgagccccaa gtctgtctgc gagggctgtc agcgggtcat cttggacagg tttctgctgc
     1141 ggctcaacga cagcttctgg catgagcagt gcgtgcagtg cgcctcctgc aaagagcccc
     1201 tggagaccac ctgcttctac cgggacaaga agctgtactg caagtatgac tacgagaagt
     1261 aagtggccgc acccccgcag cgctccccgc gcactggcat nnnnnnnnnn nnnnnnnnnn
     1321 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1381 nnnnnnnnnn nnnnnnnnnn atcccagttc ttgaagttcc ttttgctgtt gacttcaggg
     1441 gagacccagg accaagccag attttactca tggtgcatgt acttcctttc tccctgctgc
     1501 caggctgttt gctgttaaat gtgggggctg cttcgaggcc atcgctccca atgagtttgt
     1561 tatgcgggcc cagaagagtg tataccacct gagctgcttc tgctgctgtg tctgcgagcg
     1621 acagcttcag aagggtgatg agtttgtcct gaaggagggg cagctgctct gcaaagggga
     1681 ctatgagaag gagcgggagc tgctcagcct ggtgagccca gcagcctcag actcaggtga
     1741 gtgccaggtg gtgggcaggg ctgcggtggg gtgggtagag tggagttggg tggctgtctg
     1801 cattgtttct tccctagatg nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1921 catacagctc caggaactgg ctttcaggga ctcacaacat tgtcttttgc ttctttcagg
     1981 taaaagtgat gatgaagaaa gtctctgcaa gtcagcccat ggggcaggga aaggaactgc
     2041 tgaggaaggc aaggaccata agcgccccaa acgtccgaga accatcttga caactcaaca
     2101 gaggcgagca ttcaaggcct catttgaagt atcctccaag ccctgcagga aggtatagga
     2161 gggagcaggg aggaaaagga gctgggcccc acttctctgt gtgcactcag acccctctgg
     2221 gatctcagtg ggcattgggg gtcacagtgg tgaggaaggc tgttcagaca gagcctgcac
     2281 aggcggctca agcctgttgg agactccaga gatcactaag ctgtggccag ggtgtgatag
     2341 actctcctga agctttcatg catgcacacc aactccaaat ggcccctgtc acacctttca
     2401 tttcatagag cacaatggga acagtaataa tgataggtgt ccattgtggt gtagacccag
     2461 atgctgtaaa gcaaagagta taaaaacaca gtggcttgca gtactctttt ttgagtctgg
     2521 ctttttccac ttggtgtggt ggtttgggga ttcattcatt cctatttcag cattccactg
     2581 tataggtgtg ccatgattgg tttgtccatg cacctgttga tgggtgtttg gggttgtttc
     2641 tagtttggga ctgtttcaaa taggactgct atggacattc atgtaaaaaa aaatacagtg
     2701 gtttaatgag acaggagttt attctcttct gtcacagtcc agaggtgagc aaggcaaggc
     2761 tggtgggtgg ctctgttatc catctcctgt gtccaagcga ctgctccagt tgtcaccatg
     2821 tttccagtca ccaggtagag aaagaggaaa tggagggcaa gcgccctgct ttttaaggat
     2881 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     2941 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn atgcatatgc atggcttata
     3001 gctaaagcac aacaatagac taaagtctaa accacttgaa ggcctaattt ccagagcaag
     3061 agaaatccag aaacacctct tgggaatgca catgtaaatt aataattatt attttgtttc
     3121 tttacctggt gaaggacttt ctttctacct gaagggaagc aatgttctcg tgtttgtgtg
     3181 tatgctcaac attaaaaact attcagctcc taaagcagat acagtctttt ggcctcctca
     3241 agtattatat aggagatgtt ctacctccta ccctgagatg ccagtgtgtc tacatttctc
     3301 gttcaatttt tccaaggtga gagagactct ggctgcagag acagggctga gtgtccgtgt
     3361 cgtccaggtg tggttccaaa accagagagc gaaggtaacc tgcttcttac ttttatctgt
     3421 ccccatgttg ctggtttcct gaaataatca cagtaggaca nnnnnnnnnn nnnnnnnnnn
     3481 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3541 nnnnnnnnnn nnnnnnnnnn agccctctcc cggggaaggt gtcacttcca ggccccccct
     3601 tactttgtga acatgctgca ggccacctga cttctaatcc tatggtcctc tccttatcag
     3661 atgaagaagc tggccaggcg acagcagcag cagcagcaag atcagcagaa cacccagagg
     3721 ctgagctctg gtaagctggt gcctcctccc aggcagttct ggctggaatc caggctgttc
     3781 ctaccagagg cctcccacta cccagctctt tggatgacat atctggactc agtgaagcct
     3841 agaccacacc cactggagaa ataaggcctt caagggaaga ctgagccacg aggaacttgt
     3901 gagagggttg agggctcctg agctgcaggc ttagaactgc tgattgggga tggcactgac
     3961 cttatccaca gcgtccaggc ctggatccca ccacagcgtc agggactgct tgcagagtca
     4021 cagatacgtt cagtttctca tcttgcttag ttctccttcc aggctaattg atttaataga
     4081 agacacctcg gtgacttggc tctttccaaa ataacataaa gtagtaaaaa taatgatagt
     4141 aaaataacaa tgccttcctt tgttgaacac tcttatagat tggtgttctc atacatgctg
     4201 acttgacttt tacaacaccc attcctggag gcgagtggag aagttgttat tatccctatg
     4261 tcacagatga gcaaacaaag gctctgcaag attgaatgtg gccctagatc ggtaagggca
     4321 gggggctggg actagaactc taactgtgtt ccacaggcca tgggccttct catctctacc
     4381 cagatgtgct tttgaaaaag nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4441 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4501 cacgttgaga atgacctggc ttcttctttg ttccacagct cagacaaacg gtggtgggag
     4561 tgctgggatg gaaggaatca tgaaccccta cacggctctg cccaccccac agcagctcct
     4621 ggccatcgag cagagtgtct acagctcaga tcccttccga cagggtctca ccccacccca
     4681 gatgcctgga gaccacatgc acccttatgg taagagggac ttaagcccct cgggccctct
     4741 cataacttgt gtgggtttct cattccctcc taaacacatc taggcagttc ccagatgctc
     4801 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn aaatgagtca cttcttcaag
     4921 accctcatgc cagtgtttca tctccatttc aggtgccgag ccccttttcc atgacctgga
     4981 tagcgacgac acctccctca gtaacctggg tgattgtttc ctagcaacct cagaagctgg
     5041 gcctctgcag tccagagtgg gaaaccccat tgaccatctg tactccatgc agaattctta
     5101 cttcacatct tgagtcttcc cctagagttc tgtgactagg ctcccatatg gaacaaccat
     5161 attctttgag gggtcactgg ctttaggaca gggaggccag ggaagaggtg ggttggggag
     5221 ggagttttgt tggggatgct gttgtataat gatatggtgt agctcagcat ttccaaagac
     5281 tgaatacatt atggattgca tagtttaatg
//