LIM homeobox 4 (LHX4) - coding DNA reference sequence

(used for variant description)

(last modified December 24, 2022)

This file was created to facilitate the description of sequence variants on transcript NM_033343.3 in the LHX4 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000001.10, covering LHX4 transcript NM_033343.3.

Please note that introns are available by clicking on the exon numbers above the sequence.

 (upstream sequence)
           .         .         .         .         .                g.5052
         gcaccaaccccggagagcgagatcaaagggactggaaacagactggggactg       c.-181

 .         .         .         .         .         .                g.5112
 gcggggggagggggccggccagcctgtggagtcctccctgagaagcggagggcccggctt       c.-121

 .         .         .         .         .         .                g.5172
 ccaccgtgactccagcggcctgcttggggttttaattattattttgaaatttctgaatcg       c.-61

 .         .         .         .         .         .                g.5232
 agctagagcgagagagcgagagatctccgtagactgcgactcgctggctttcgctccgag       c.-1

          .         .         .         .         .         .       g.5292
 ATGATGCAGAGTGCGACTGTCCCCGCGGAAGGGGCTGTCAAGGGGCTCCCGGAGATGCTA       c.60
 M  M  Q  S  A  T  V  P  A  E  G  A  V  K  G  L  P  E  M  L         p.20

          .       | 02 .         .         .         .         .    g.23031
 GGTGTGCCGATGCAAC | AGATTCCCCAGTGCGCTGGCTGCAACCAGCACATCCTGGACAAG    c.120
 G  V  P  M  Q  Q |   I  P  Q  C  A  G  C  N  Q  H  I  L  D  K      p.40

          .         .         .         .         .         .       g.23091
 TTCATCCTGAAGGTCCTGGACAGACACTGGCACAGCTCCTGCCTCAAGTGTGCAGACTGC       c.180
 F  I  L  K  V  L  D  R  H  W  H  S  S  C  L  K  C  A  D  C         p.60

          .         .         .         .         .         .       g.23151
 CAGATGCAGCTGGCGGACAGGTGCTTCTCCAGGGCTGGGAGCGTCTACTGCAAGGAGGAC       c.240
 Q  M  Q  L  A  D  R  C  F  S  R  A  G  S  V  Y  C  K  E  D         p.80

          | 03         .         .         .         .         .    g.41146
 TTCTTCAA | GCGCTTCGGCACAAAATGCACGGCCTGCCAGCAGGGTATCCCCCCAACCCAG    c.300
 F  F  K  |  R  F  G  T  K  C  T  A  C  Q  Q  G  I  P  P  T  Q      p.100

          .         .         .         .         .         .       g.41206
 GTGGTCCGCAAGGCCCAGGACTTTGTCTACCACCTGCACTGCTTTGCTTGCATCATCTGC       c.360
 V  V  R  K  A  Q  D  F  V  Y  H  L  H  C  F  A  C  I  I  C         p.120

          .         .         .         .         .         .       g.41266
 AACCGGCAGCTGGCCACGGGGGACGAATTCTACCTCATGGAGGACGGGCGGCTGGTGTGC       c.420
 N  R  Q  L  A  T  G  D  E  F  Y  L  M  E  D  G  R  L  V  C         p.140

          .         .         .  | 04      .         .         .    g.46111
 AAGGAAGACTACGAGACAGCCAAGCAGAACG | ATGACTCAGAGGCTGGAGCTAAGCGGCCC    c.480
 K  E  D  Y  E  T  A  K  Q  N  D |   D  S  E  A  G  A  K  R  P      p.160

          .         .         .         .         .         .       g.46171
 CGGACCACCATCACAGCCAAGCAGCTGGAGACATTAAAGAATGCATACAAGAACTCCCCC       c.540
 R  T  T  I  T  A  K  Q  L  E  T  L  K  N  A  Y  K  N  S  P         p.180

          .         .         .         .         .         .       g.46231
 AAGCCTGCCCGGCACGTGAGGGAGCAGCTGTCCTCAGAGACAGGCCTGGACATGAGGGTC       c.600
 K  P  A  R  H  V  R  E  Q  L  S  S  E  T  G  L  D  M  R  V         p.200

        | 05 .         .         .         .         .         .    g.46591
 GTACAG | GTTTGGTTTCAGAACAGAAGGGCCAAAGAGAAACGCCTGAAGAAGGATGCAGGG    c.660
 V  Q   | V  W  F  Q  N  R  R  A  K  E  K  R  L  K  K  D  A  G      p.220

          .         .         .         .         .         .       g.46651
 CGGCACCGCTGGGGGCAGTTCTATAAGAGCGTCAAGAGGAGCCGGGGCAGCAGCAAGCAG       c.720
 R  H  R  W  G  Q  F  Y  K  S  V  K  R  S  R  G  S  S  K  Q         p.240

          .         .         .         .         .         | 06    g.48889
 GAGAAGGAGAGCTCTGCAGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG | AG    c.780
 E  K  E  S  S  A  E  D  C  G  V  S  D  S  E  L  S  F  R  E |       p.260

          .         .         .         .         .         .       g.48949
 GATCAAATTCTCTCAGAACTTGGCCACACCAATAGGATTTATGGCAACGTGGGGGACGTT       c.840
 D  Q  I  L  S  E  L  G  H  T  N  R  I  Y  G  N  V  G  D  V         p.280

          .         .         .         .         .         .       g.49009
 ACAGGCGGACAGTTAATGAATGGGAGCTTCTCCATGGACGGGACAGGACAATCCTATCAG       c.900
 T  G  G  Q  L  M  N  G  S  F  S  M  D  G  T  G  Q  S  Y  Q         p.300

          .         .         .         .         .         .       g.49069
 GACTTGAGGGATGGGAGCCCCTATGGAATCCCCCAGTCTCCATCCTCCATATCGTCCCTG       c.960
 D  L  R  D  G  S  P  Y  G  I  P  Q  S  P  S  S  I  S  S  L         p.320

          .         .         .         .         .         .       g.49129
 CCATCCCACGCTCCTTTGCTCAATGGGCTGGATTACACGGTGGACAGTAATTTGGGCATC       c.1020
 P  S  H  A  P  L  L  N  G  L  D  Y  T  V  D  S  N  L  G  I         p.340

          .         .         .         .         .         .       g.49189
 ATTGCGCATGCAGGGCAGGGAGTAAGCCAGACGCTGAGAGCCATGGCTGGGGGACCCACC       c.1080
 I  A  H  A  G  Q  G  V  S  Q  T  L  R  A  M  A  G  G  P  T         p.360

          .         .         .         .         .         .       g.49249
 TCTGACATCTCCACAGGAAGCAGTGTAGGCTATCCCGACTTTCCAACTAGCCCAGGCTCT       c.1140
 S  D  I  S  T  G  S  S  V  G  Y  P  D  F  P  T  S  P  G  S         p.380

          .         .         .                                     g.49282
 TGGCTCGATGAAATGGATCATCCTCCTTTTTAA                                  c.1173
 W  L  D  E  M  D  H  P  P  F  X                                    p.390

          .         .         .         .         .         .       g.49342
 acttctctcctccccaccctacctgcccccctggcttgagagaatatcttcaaggatcaa       c.*60

          .         .         .         .         .         .       g.49402
 aagagacttgccttttaaggatcgaaagtacgccaatgtgaatttccattattttcaatg       c.*120

          .         .         .         .         .         .       g.49462
 gaagtcctccgctgattcctagaaggctgtgagaccacactagggcattgtttccctggg       c.*180

          .         .         .         .         .         .       g.49522
 gaagcagtgggagagcagactcatctcagaacacagcacagggggtaatggcctagagct       c.*240

          .         .         .         .         .         .       g.49582
 ctagggacactggcttgttgggtctctcccctgctgttctgcttaggggcttggctgctc       c.*300

          .         .         .         .         .         .       g.49642
 agtgctttggtagcacaaggtgactgtgataggcccccttggcctttgggaactttgctc       c.*360

          .         .         .         .         .         .       g.49702
 caactggtgtgtctcacacaatgcctcccaaaacactgctctcaccagaactgagactcc       c.*420

          .         .         .         .         .                 g.49756
 taaggtagaggcctcacagcccttgagtaaaataaaagtgatttctggaccatc             c.*474

 (downstream sequence)

Legend:
Nucleotide numbering (following the rules of the HGVS for a 'Coding DNA Reference Sequence') is indicated at the right of the sequence, counting the A of the ATG translation initiating Methionine as 1. Every 10^th nucleotide is indicated by a "." above the sequence. The LIM homeobox 4 protein sequence is shown below the coding DNA sequence, with numbering indicated at the right starting with 1 for the translation initiating Methionine. Every 10^th amino acid is shown in bold. The position of introns is indicated by a vertical line, splitting the two exons. The start of the first exon (transcription initiation site) is indicated by a '\', the end of the last exon (poly-A addition site) by a '/'. The exon number is indicated above the first nucleotide(s) of the exon. To aid the description of frame shift variants, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.