Analyses of Ribosomal Protein (RP) Pseudogenes in Human Genome

We have identified over 2000 ribosomal protein (RP) pseudogenes in the August 2001 freeze of the human genome draft. An interactive database holding all the results is being constructed. Meanwhile, the relevant data and texts can be found here.

- Reference:

- Figure:

• compressed sequence data
• compressed sequence alignment files

• Nomenclature table  cross-listing the yeast, rat and human gene name and SWISSPROTE IDs
• Excel version of the nomenclature table  which also lists the mRNA and CDS length
• Ascii text version of the table
• RP mRNA seuqence files from GenBank
• RP mRNA CDS (protein coding sequence) files frlom GenBank

Alignments

• Alignment files of RP pseudogene CDS sequences (processed only) together with corresponding functional  RP gene sequence using ClustalW.
• ClustalW website

Annotation files

• An Excel file (1.81Mb) and text file (0.4Mb) containing annotation for pseudogenes in the whole human genome
• An Excel file (30Kb) listing number of pseudogenes for each one of the 80 RP genes
• sorted by chromosomes
• sorted by RP gene IDs

DNA sequence files

master files (containing data for all pseudogenes in the genome)

• CDS (all)  
• CDS plus 500 bp beyond both ends, including UTR and flanking region  
• CDS plus 1000 bp beyond both ends, including UTR and flanking region  
• 5' sequence (including 60 bp in the CDS region and 100 bp beyond 5'  
• 5' sequence (including 60 bp in the CDS region and 500 bp beyond 5'  
• 5' sequence (including 60 bp in the CDS region and 1000 bp beyond 5'  
• 3' sequence (including 60 bp in the CDS region and 100 bp beyond 3'  
• 3' sequence (including 60 bp in the CDS region and 500 bp beyond 3'  
• 3' sequence (including 60 bp in the CDS region and 1000 bp beyond 3'  

sorted by chromosomes

• CDS
• CDS plus 100 bp beyond both ends, including UTR and flanking region
• CDS plus 500 bp beyond both ends, including UTR and flanking region
• CDS plus 1000 bp beyond both ends, including UTR and flanking region
• 5' sequence (including 60 bp in the CDS region and 100 bp beyond 5')
• 5' sequence (including 60 bp in the CDS region and 500 bp beyond 5')
• 5' sequence (including 60 bp in the CDS region and 1000 bp beyond 5')
• 3' sequence (including 60 bp in the CDS region and 100 bp beyond 3')
• 3' sequence (including 60 bp in the CDS region and 500 bp beyond 3')
• 3' sequence (including 60 bp in the CDS region and 1000 bp beyond 3')

sorted by rp gene IDs

• CDS
• CDS plus 100 bp beyond both ends, including UTR and flanking region
• CDS plus 500 bp beyond both ends, including UTR and flanking region
• CDS plus 1000 bp beyond both ends, including UTR and flanking region
• 5' sequence (including 60 bp in the CDS region and 100 bp beyond 5')
• 5' sequence (including 60 bp in the CDS region and 500 bp beyond 5')
• 5' sequence (including 60 bp in the CDS region and 1000 bp beyond 5')
• 3' sequence (including 60 bp in the CDS region and 100 bp beyond 3')
• 3' sequence (including 60 bp in the CDS region and 500 bp beyond 3')
• 3' sequence (including 60 bp in the CDS region and 1000 bp beyond 3')

Amino acid sequence files

For each pseudogene, the aligned functional RP aa sequences are also listed.

• RP pseudogene translated amino acid file (1.0 Mb) containing pseudogenes in the whole human genome.
• sorted by chromosome
• sorted by RP gene