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

Note regarding MECP2 mutation nomenclature: Historically, MECP2 variants were called based on the e2 isoform (i.e. transcript containing exons 1, 2, 3 & 4, with start codon in exon 2)and RettBASE displayed variants predominantly in e2 isoform. RettBASE has since updated the MECP2 database to include variants in e1 isoform (NM_001110792.1). Users can now change the transcript of interest in list of all variants to view variants in each transcript. The variant and proband pages has also been updated to reflect variant nomenclature in both transcripts. For information regarding reference sequence for MECP2, please visit our reference sequence page. Also please see our nomenclature section for general guidelines for mutation nomenclature.

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: