LIM homeobox 2 (LHX2) - coding DNA reference sequence

(used for variant description)

(last modified December 16, 2022)

This file was created to facilitate the description of sequence variants on transcript NM_004789.3 in the LHX2 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000009.11, covering LHX2 transcript NM_004789.3.

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

 (upstream sequence)
                                                   .                g.5019
                                          gactgcagagccggggctg       c.-721

 .         .         .         .         .         .                g.5079
 ggctaggcgcgcgcttggagagcattgcgcgcggctgggcccgcggccggcggctcctcc       c.-661

 .         .         .         .         .         .                g.5139
 tcccactctgctcctcctcttttttctcctcctccacctcctcctccgcctcctcctcct       c.-601

 .         .         .         .         .         .                g.5199
 cctcttcctcctcctcttcaattctcccggtggctcgactcggctcgcaggcttcggaga       c.-541

 .         .         .         .         .         .                g.5259
 aacccctactccagtcgccgactcagcgcccaagagggtcgccttgggctgggggcgcac       c.-481

 .         .         .         .         .         .                g.5319
 cccagggaggggaggggtccaggcagctgggccgccgcggacacctagcggcttcagggt       c.-421

 .         .         .         .         .         .                g.5379
 gaaccccgaccgcagccgtcgccgcctcgggcagagtttgcgcccttgctttgcgccccg       c.-361

 .         .         .         .         .         .                g.5439
 ggcgctgaagccgggcgggcgatgcccgcggcgtgaaagcgcccgcggcgggcgccgacc       c.-301

 .         .         .         .         .         .                g.5499
 tctgtcctagtctcctgctccccccgccccgcttgtcccgtgcccttgtgaccctggctt       c.-241

 .         .         .         .         .         .                g.5559
 tggcgccgtcgcccaggcgccccgcaatgtagctgcccctgcgcctcggcgggaggcgtc       c.-181

 .         .         .         .         .         .                g.5619
 ctgccccgcgagcgcccggggcccggagcccggcctgggggctcagccgagctcgggcgg       c.-121

 .         .         .         .         .         .                g.5679
 ggccggggccgcggtggcgatgcaccgggcccgttagcgccaggagcgccaggcagctga       c.-61

 .         .         .         .         .         .                g.5739
 ggcggggggcaagccctccctcggaggagccgcgcccccggccccgccggtcccgccgcg       c.-1

          .         .         .         .         .         .       g.5799
 ATGCTGTTCCACAGTCTGTCGGGCCCCGAGGTGCACGGGGTCATCGACGAGATGGACCGC       c.60
 M  L  F  H  S  L  S  G  P  E  V  H  G  V  I  D  E  M  D  R         p.20

          .         .         .         .         .         .       g.5859
 AGGGCCAAGAGCGAGGCTCCCGCCATCAGCTCCGCCATCGACCGCGGCGACACCGAGACG       c.120
 R  A  K  S  E  A  P  A  I  S  S  A  I  D  R  G  D  T  E  T         p.40

  | 02       .         .         .         .         .         .    g.7411
  | ACCATGCCGTCCATCAGCAGTGACCGCGCCGCGCTGTGCGCCGGCTGCGGGGGCAAGATC    c.180
  | T  M  P  S  I  S  S  D  R  A  A  L  C  A  G  C  G  G  K  I      p.60

          .         .         .         .         .         .       g.7471
 TCGGACCGCTACTACCTGCTGGCGGTGGACAAGCAGTGGCACATGCGCTGCCTCAAGTGC       c.240
 S  D  R  Y  Y  L  L  A  V  D  K  Q  W  H  M  R  C  L  K  C         p.80

          .         .         .         .         .         .       g.7531
 TGCGAGTGCAAGCTCAACCTGGAGTCGGAGCTCACCTGTTTCAGCAAGGACGGTAGCATC       c.300
 C  E  C  K  L  N  L  E  S  E  L  T  C  F  S  K  D  G  S  I         p.100

          .         .    | 03    .         .         .         .    g.8549
 TACTGCAAGGAAGACTACTACAG | GCGCTTCTCTGTGCAGCGCTGCGCCCGCTGCCACCTG    c.360
 Y  C  K  E  D  Y  Y  R  |  R  F  S  V  Q  R  C  A  R  C  H  L      p.120

          .         .         .         .         .         .       g.8609
 GGCATCTCGGCCTCGGAGATGGTGATGCGCGCTCGGGACTTGGTTTATCACCTCAACTGC       c.420
 G  I  S  A  S  E  M  V  M  R  A  R  D  L  V  Y  H  L  N  C         p.140

          .         .         .         .         .         .       g.8669
 TTCACGTGCACCACGTGTAACAAGATGCTGACCACGGGCGACCACTTCGGCATGAAGGAC       c.480
 F  T  C  T  T  C  N  K  M  L  T  T  G  D  H  F  G  M  K  D         p.160

          .         .         .         .         .         .       g.8729
 AGCCTGGTCTACTGCCGCTTGCACTTCGAGGCGCTGCTGCAGGGCGAGTACCCCGCACAC       c.540
 S  L  V  Y  C  R  L  H  F  E  A  L  L  Q  G  E  Y  P  A  H         p.180

          .         .         .         .         .         .       g.8789
 TTCAACCATGCCGACGTGGCAGCGGCGGCCGCTGCAGCCGCGGCGGCCAAGAGCGCGGGG       c.600
 F  N  H  A  D  V  A  A  A  A  A  A  A  A  A  A  K  S  A  G         p.200

          .         .         .         .         .         .       g.8849
 CTGGGCGCAGCAGGGGCCAACCCTCTGGGTCTTCCCTACTACAATGGCGTGGGCACTGTG       c.660
 L  G  A  A  G  A  N  P  L  G  L  P  Y  Y  N  G  V  G  T  V         p.220

          .         .         .         .         .         .       g.8909
 CAGAAGGGGCGGCCGAGGAAACGTAAGAGCCCGGGCCCCGGTGCGGATCTGGCGGCCTAC       c.720
 Q  K  G  R  P  R  K  R  K  S  P  G  P  G  A  D  L  A  A  Y         p.240

         | 04.         .         .         .         .         .    g.14542
 AACGCTG | CGCTAAGCTGCAACGAAAACGACGCAGAGCACCTGGACCGTGACCAGCCATAC    c.780
 N  A  A |   L  S  C  N  E  N  D  A  E  H  L  D  R  D  Q  P  Y      p.260

          .         .         .         .         .         .       g.14602
 CCGAGCAGCCAGAAGACCAAGCGCATGCGCACGTCCTTCAAGCACCACCAGCTTCGGACC       c.840
 P  S  S  Q  K  T  K  R  M  R  T  S  F  K  H  H  Q  L  R  T         p.280

          .         .         .         .         .         .       g.14662
 ATGAAGTCTTACTTTGCCATTAACCACAACCCCGACGCCAAGGACTTGAAGCAGCTCGCG       c.900
 M  K  S  Y  F  A  I  N  H  N  P  D  A  K  D  L  K  Q  L  A         p.300

          .         .         .    | 05    .         .         .    g.25837
 CAAAAGACGGGCCTCACCAAGCGGGTCCTCCAG | GTCTGGTTCCAGAACGCCCGAGCCAAG    c.960
 Q  K  T  G  L  T  K  R  V  L  Q   | V  W  F  Q  N  A  R  A  K      p.320

          .         .         .         .         .         .       g.25897
 TTCAGGCGCAACCTCTTACGGCAGGAAAACACGGGCGTGGACAAGTCGACAGACGCGGCG       c.1020
 F  R  R  N  L  L  R  Q  E  N  T  G  V  D  K  S  T  D  A  A         p.340

          .         .         .         .         .         .       g.25957
 CTGCAGACAGGGACGCCATCGGGCCCGGCCTCGGAGCTCTCCAACGCCTCGCTCAGCCCC       c.1080
 L  Q  T  G  T  P  S  G  P  A  S  E  L  S  N  A  S  L  S  P         p.360

          .         .         .         .         .         .       g.26017
 TCCAGCACGCCCACCACCCTGACAGACTTGACTAGCCCCACCCTGCCAACTGTGACGTCC       c.1140
 S  S  T  P  T  T  L  T  D  L  T  S  P  T  L  P  T  V  T  S         p.380

          .         .         .         .         .         .       g.26077
 GTCTTAACTTCTGTGCCTGGCAACCTGGAGGGCCATGAGCCTCACAGCCCCTCACAAACG       c.1200
 V  L  T  S  V  P  G  N  L  E  G  H  E  P  H  S  P  S  Q  T         p.400

          .         .                                               g.26098
 ACTCTTACCAACCTTTTCTAA                                              c.1221
 T  L  T  N  L  F  X                                                p.406

          .         .         .         .         .         .       g.26158
 tgactcgcaacccctcaccccacaatttctttaaaaaagaaattatctttagttgaattc       c.*60

          .         .         .         .         .         .       g.26218
 caagtgtattttaaaatagaggctttgagcaactaactaaccacattttaggatctcgcc       c.*120

          .         .         .         .         .         .       g.26278
 tggaaacagaggtaaaaaaaagaagtgtgcgcccggctaatgcagcggtgtggaccgagg       c.*180

          .         .         .         .         .         .       g.26338
 aacaacttggaagatctacctgcaacacaacatttgtgtcactgtacagttttgtggact       c.*240

          .         .         .         .         .         .       g.26398
 gagcgaggaaaaacaacaaataatttaagttggctagagcttctgtattttcaaagactg       c.*300

          .         .         .         .         .         .       g.26458
 ccacgtgccttaggaatactgttttatctccatactttggatgacttgttcatttttctc       c.*360

          .         .         .         .         .         .       g.26518
 tccctctttttctctgtatatttatgaccagagcaaaaatgtaaaaaacaaaaaaaacaa       c.*420

          .         .         .                                     g.26554
 caaaaaaagtttgttactttgaatagtcctaaaaag                               c.*456

 (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 2 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.