The tables chr21.pseudogenes and chr22.pseudogenes contain pseudogene 
annotations. All annotations are for individual exons, except where labelled 
'multi_exon' in the comment field. 


This data is unpublished and may be modified again before publication. 
Please do not disseminate it. 


The fields of the tables are as follows:

1 = chromosome label. 
    Either chr21_ or chr22_. 

2 = source of the pseudogene. 
    Either pmh (annotations derived here, abbreviation for 'pseudomatch' ) or sanger (Sanger Center annotations) 

3 = sequence type. 
    Swp (derived from matching SWISSPROT protein) ; Ens (derived from matching Ensembl protein) ; sanger (derived 
    from Sanger centre annotation) 

4 = start of sequence on chromosome. 

5 = end of sequence on chromosome.  

6 = strand of chromosome.  

7 = primary name of the sequence.  

8 = number of exons for the pseudogene (Sanger Center chromosome 22 annotations).  

9 = classification according to detection of polyadenylation. 
    Class '1' if have AATAAA signal <50 nt 5' to polyadenine tail ; 
    Class '2' if have AATAAA signal <100 && >=50 nt 5' to polyadenine tail (very few of these); 
    Class '3' if have polyadenine tail but no AATAAA signal ; 
    else labelled '-1' 

10 = fraction of length of closest matching sequence (Ensembl, and if no Ensembl matcher, the closest 
     SWISSPROT matcher). 
 
11 = long or short segment. 
     equal to 1, if length >95% of known exons for human chromosome 22 genes (>942 nt) 
     equal to -1, otherwise 

12 = whether Ig segment. 
     equal to 1, if immunoglobulin gene segment 
     equal to 0, otherwise 

13 = length of largest gap in closes sequence (in aa). 

14 = whether candidate processed pseudogene 
     equal to 1, if candidate processed pseudogene 
     equal to 0, otherwise 

15 = comment on entry (labelled 'multi_exon' if largest gap in the pseudogene is >126 nt; 5% of introns would be shorter than this)
     other labels are 'pssd_pgene' (processed pseudogene), 'ig_segment' (immunoglobulin gene segment) 
     and 'single_exon'.       

16 = alternative name for sequence (sometimes used)

17 = name of closest Ensembl human protein matcher, if any 

18 = percentage identity to closest Ensembl human protein matcher, if any  

19 = OLD or NEW (< or >=79% id to closest Ensembl human protein matcher) 

20 = overall name (different to primary name for individual pseudogenic matches 
     that have been merged into one pseudogene by inspection) 

21 = list of InterPro motif names for this pseudogene

22 = list of GO classifications for this pseudogene 


#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*# 



The corresponding files of sequences for the pseudogenes that I have derived
are in (fasta format, the name is the 'primary name' given above):

(chromosome 21) 
chr21.pmh.Swp.N.FASTA ---> pseudogenes for which the primary match is to a SWISSPROT protein 
chr21.pmh.Ens.N.FASTA ---> pseudogenes for which the primary match is to an Ensembl protein 
chr21.riken.pmh.N.FASTA ---> pseudogenes which are primarily Riken Centre annotations, but 
which are also detected by our procedures. 

(chromosome 22) 
chr22.pmh.Swp.N.FASTA ---> pseudogenes for which the primary match is to a SWISSPROT protein
chr22.pmh.Ens.N.FASTA ---> pseudogenes for which the primary match is to an Ensembl protein  
chr22.sanger.pmh.N.FASTA ---> pseudogenes which are primarily Sanger Centre annotations, but 
which are also detected by our procedures. 


Frameshifts are indicated by a slash ('/' or '\') and a deletion by a '-'. Stops are 
labelled with an '*'.