linker for activation of T cells (LAT) - coding DNA reference sequence

(used for variant description)

(last modified May 23, 2022)

This file was created to facilitate the description of sequence variants on transcript NM_001014987.1 in the LAT gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000016.9, covering LAT transcript NM_001014987.1.

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

 (upstream sequence)
           .         .         .         .         .                g.5292
         caggcgggcgggagggcgggcacggagaggcgggcgccgaggaggggcaggt       c.-301

 .         .         .         .         .         .                g.5352
 agggctgggacgcaggggtaactggatcccccgacttcagcccaggccctggtctgacca       c.-241

 .         .         .         .         .         .                g.5412
 ccctgggagcagggactttccacagtcagctggacgcacactcagcccagtaaaagaggg       c.-181

 .         .         .         .         .         .                g.5472
 gacccatcccgggagccccggggagggcacagctgcctcctcccgggctcccctgccacc       c.-121

 .         .         .         .         .         .                g.5532
 tggtgcctacctgccccctgctccctgccgggtccggtcctcaccccatcttcatctggc       c.-61

 .         .         .         .         .         .                g.5592
 cttgactctgcccttgaggggcctaggggtgcagccagcctgctccgagctcccctgcag       c.-1

          .         .         .         .         .         .       g.5652
 ATGGAGGAGGCCATCCTGGTCCCCTGCGTGCTGGGGCTCCTGCTGCTGCCCATCCTGGCC       c.60
 M  E  E  A  I  L  V  P  C  V  L  G  L  L  L  L  P  I  L  A         p.20

          .         .         .         . | 02       .         .    g.5907
 ATGTTGATGGCACTGTGTGTGCACTGCCACAGACTGCCAG | GCTCCTACGACAGCACATCC    c.120
 M  L  M  A  L  C  V  H  C  H  R  L  P  G |   S  Y  D  S  T  S      p.40

          | 03         .         .         .    | 04    .         . g.6326
 TCAGATAG | TTTGTATCCAAGGGGCATCCAGTTCAAACGGCCTC | ACACGGTTGCCCCCTGG c.180
 S  D  S  |  L  Y  P  R  G  I  Q  F  K  R  P  H |   T  V  A  P  W   p.60

          .         .         .         .         .         .       g.6386
 CCACCTGCCTACCCACCTGTCACCTCCTACCCACCCCTGAGCCAGCCAGACCTGCTCCCC       c.240
 P  P  A  Y  P  P  V  T  S  Y  P  P  L  S  Q  P  D  L  L  P         p.80

       | 05  .         .         .         .         .         .    g.6611
 ATCCC | AAGATCCCCGCAGCCCCTTGGGGGCTCCCACCGGACGCCATCTTCCCGGCGGGAT    c.300
 I  P  |  R  S  P  Q  P  L  G  G  S  H  R  T  P  S  S  R  R  D      p.100

          . | 06       .         .         . | 07       .         . g.6851
 TCTGATGGTG | CCAACAGTGTGGCGAGCTACGAGAACGAGG | AACCAGCCTGTGAGGATGCG c.360
 S  D  G  A |   N  S  V  A  S  Y  E  N  E  E |   P  A  C  E  D  A   p.120

          .         .         .         | 08         .         .    g.6995
 GATGAGGATGAGGACGACTATCACAACCCAGGCTACCT | GGTGGTGCTTCCTGACAGCACC    c.420
 D  E  D  E  D  D  Y  H  N  P  G  Y  L  |  V  V  L  P  D  S  T      p.140

          .         .         .         .         .         .       g.7055
 CCGGCCACTAGCACTGCTGCCCCATCAGCTCCTGCACTCAGCACCCCTGGCATCCGAGAC       c.480
 P  A  T  S  T  A  A  P  S  A  P  A  L  S  T  P  G  I  R  D         p.160

          .    | 09    .         .         .         .         .    g.9748
 AGTGCCTTCTCCA | TGGAGTCCATTGATGATTACGTGAACGTTCCGGAGAGCGGGGAGAGC    c.540
 S  A  F  S  M |   E  S  I  D  D  Y  V  N  V  P  E  S  G  E  S      p.180

          .       | 10 .         .         .         .         .    g.9992
 GCAGAAGCGTCTCTGG | ATGGCAGCCGGGAGTATGTGAATGTGTCCCAGGAACTGCATCCT    c.600
 A  E  A  S  L  D |   G  S  R  E  Y  V  N  V  S  Q  E  L  H  P      p.200

          .         .   | 11     .         .         .         .    g.10145
 GGAGCGGCTAAGACTGAGCCTG | CCGCCCTGAGTTCCCAGGAGGCAGAGGAAGTGGAGGAA    c.660
 G  A  A  K  T  E  P  A |   A  L  S  S  Q  E  A  E  E  V  E  E      p.220

          .         .         .         .                       g.10187
 GAGGGGGCTCCAGATTACGAGAATCTGCAGGAGCTGAACTGA |                      c.703
 E  G  A  P  D  Y  E  N  L  Q  E  L  N  X                        p.233

         | 12.         .         .         .         .         .    g.10416
 gggcctg | tggaggccgagtctgtcctggaaccaggcttgcctgggacggctgagctgggc    c.*60

          .         .         .         .         .         .       g.10476
 agctggaagtggctctggggtcctcacatggcgtcctgcccttgctccagcctgacaaca       c.*120

          .         .         .         .         .         .       g.10536
 gcctgagaaatccccccgtaacttattatcactttggggttcggcctgtgtcccccgaac       c.*180

          .         .         .         .         .         .       g.10596
 gctctgcaccttctgacgcagcctgagaatgacctgccctggccccagccctactctgtg       c.*240

          .         .         .         .         .         .       g.10656
 taatagaataaaggcctgcgtgtgtctgtgttgagcgtgcgtctgtgtgtgcctgtgtgc       c.*300

          .         .         .         .         .         .       g.10716
 gagtctgagtcagagatttggagatgtctctgtgtgtttgtgtgtatctgtgggtctcca       c.*360

          .         .         .         .         .         .       g.10776
 tcctccatgggggctcagccaggtgctgtgacaccccccttctgaatgaagccttctgac       c.*420

          .         .         .         .         .         .       g.10836
 ctgggctggcactgctgggggtgaggacacattgccccatgagacagtcccagaacacgg       c.*480

          .         .         .         .         .         .       g.10896
 cagctgctggctgtgacaatggtttcaccatccttagaccaagggatgggacctgatgac       c.*540

          .         .         .         .         .         .       g.10956
 ctgggaggactctcttagttcttaccttttgtggttctcaataaaacagaacttaaaaaa       c.*600

                                                                    g.10958
 tt                                                                 c.*602

 (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 Linker for activation of T cells 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.