1. ENCODE pseudogene updates Adam Frankish, HAVANA 6/10/05

2. Not added - AK125808 The transcripts on which this pseudogene is based do not appear to have a valid translation (only BC007286.1 has a translation which looks spurious) Reverse strand mRNAs Ral-GDS related protein Rgr (Rgr) pseudogene Translation

3. Not added - YalePgene_139 I have been able to reconstruct a coding gene with a full length CDS at this locus (AC009892.1) and would not annotate a coding gene and pseudogene at the same locus as discussed previously. The majority of the gene (3' end of exon 3 to final exon (8)) is supported by 100% matching (best in genome hits) human EST (Em:DN998408.1, Em:BG743947.1) and mRNA evidence (Em:BC033195.1) which together support a structure (although there is a small gap in support in exon 5) with an ORF extending from start to the final exon. Using human ESTs not from this locus eg Em:BM918119.1 (approx 70% ID at this locus best hit in genome 100% to the KIR2DL4 gene also on chr19 by ensembl SSAHA) the 5' end of exon 3 and two further upstream exons can be clearly identified (all splice sites are clearly intact). The structure contains a CDS which starts in exon 1 (shares homology with the N-terminal sequence of several KIR2D family members in the exon), ends in the final exon and contains three immunoglobulin domains. The fact that despite the lack of transcript evidence from the 5’ end locus and the quite high degree of divergence between this locus and other gene family members, these splice sites are preserved suggests that this structure is correct and a coding gene rather than a pseudogene.

4. Not added - YalePgene_139 ProteinESTmRNA Supporting evidence

5. Not added - YalePgene_139 Dot plot of EST Splice donor

6. Havana+, Yale-, UCSC- AC006326.4-001 AC006326.2-001 AC063976.2-001 AF277315.12-001 RP11-143H17.1-001 AC009892.5-001 Z84721.2-001 Z84721.4-001 AC103710.2-001 AC103710.4-001 AC129505.5-001 AC087380.10-001 AC087380.14-001 AC002456.1-001 AC009404.5-001 AC114812.7-001 AC011330.5-001 AC011330.8-001 AL162151.3-001 We think the annotation of these as pseduogenes can be supported

7. ENm001 - AC006326.2, AC006326.4 heterogeneous nuclear ribonucleoprotein A1 (Hnrpa1) pseudogene NADH dehydrogenase 2 (MTND2) pseudogene NADH dehydrogenase 4 (MTND4) pseudogene Yale pseudo UCSC pseudo New cytochrome b (CYTB) pseudogene

8. ENm002 - AC063976.2 Dot plot Alignment

9. ENm004 - RP1-127L4.3 UCSC pseudo Yale pseudo HAVANA pseudo

10. ENm006 - AF277315.12 olfactory receptor family pseudogene

11. ENm006 - RP11-143H17.1 HAVANA pseudo Frameshift

12. ENm007 - AC009892.5 HAVANA LIR pseudogene

13. ENm008 - Z84721.4 HAVANA hemoglobin, alpha pseudogene

14. ENm009 - AC103710.2 olfactory receptor, family 51, subfamily N, member 1 pseudogene Frameshift

15. ENm009 - AC103710.4 olfactory receptor, family 52, subfamily Y, member 1 pseudogene

16. ENm009 - AC129505.5 olfactory receptor, family 52, subfamily Z, member 1 pseudogene No Met First possible Met

17. ENm009 - AC087380.10 olfactory receptor, family 51, subfamily A, member 10 pseudogene Frameshift

18. ENm009 - AC087380.14 Novel pseudogene

19. ENm013 - AC002456.1 ribosomal protein L5 (RPL5) pseudogene

20. ENr121 - AC009404.5 5-hydroxytryptamine (serotonin) receptor 5B (HTR5B) pseudogene Frameshift

21. ENr131 - AC114812.7 UDP glycosyltransferase 1 family, polypeptide A2 pseudogene Frameshift

22. ENr233 - AC011330.5 Novel pseudogene 3’ truncation ~350aa missing, no stop

23. ENr233 - AC011330.8 stereocilin (STRC) pseudogene Stop codon in exon 20

24. ENr322 - AL162151.3 pseudogene similar to part of ribosomal protein L3 (RPL3) Protein dot plot mRNA dot plot