Human reference sequences

Gene Genomic sequence cDNA sequence Protein sequence
MECP2 (isoform e2) AF030876 NM_004992 NP_004983
MECP2 (isoform e1) NG_007107 NM_001110792 NP_001104262
CDKL5 (isoform1)(CDKL5115) NG_008475 NM_003159 NP_003150
CDKL5 (isoform2)(CDKL5107) NG_008475 NM_001323289.1 NP_001310218.1
FOXG1 NG_009367 NM_005249 NP_005240

Historically, MECP2 variants are called based on the e2 isoform (i.e. transcript containing exons 1, 2, 3 & 4, with start codon in exon 2). MECP2 variants in RettBASE are also named according to this convention, except for those directly affecting the e1 isoform (which will include the prefix MECP2_e1). Nomenclature of mutations in exon 3 and exon 4 will differ by 12 amino acids between the two isoforms (e.g. p.R306C or p.Arg306Cys in isoform e2 is equivalent to p.R318C or p.Arg318Cys in isoform e2). cDNA nomenclature will differ by 36 nucleotides.

Two refseq transcripts are available for CDKL5. Alternate exons for CDKL5 have been described (see Hector et al., 2016,Williamson et al., 2012, Fichou et al., 2011 and Rademacher et al., 2011 for details) but are not included in either reference sequence. Also refer to Diebold et al., 2014 regarding pathogenicity of CDKL5 variants in exons 19, 20 and 21.

Please check our resources pages for general information on mutation nomenclature.

MeCP2 sequence alignment

MeCP2 protein alignments that have previously featured on RettBASE are no longer available. The reason behind their removal relates to the reliability of the sequence data that was used at the time of the alignment. Since 2001, many genomes have been published, with high quality reference sequences for MECP2 and conservation information now available through public domains such as National Center for Biotechnology Information (NCBI), UCSC Genome Browser, Ensembl, European Bioinformatics Instititue (EMBL-EBI) and many more.

Users interested in MeCP2 protein alignments may find the following links of use: