ENCODE pseudogene updates Adam Frankish, HAVANA 13/10/05

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

Not added - YalePgene_139 I have been able to reconstruct a coding gene with a full length CDS at this locus (AC ) 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:DN , Em:BG ) and mRNA evidence (Em:BC ) 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:BM (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.

Not added - YalePgene_139 ProteinESTmRNA Supporting evidence

Not added - YalePgene_139 Dot plot of EST Splice donor

Havana+, Yale-, UCSC- AC AC AC AF RP11-143H AC Z Z AC AC AC AC AC AC AC AC AC AC AL We think the annotation of these as pseduogenes can be supported

ENm001 - AC , AC 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

ENm002 - AC Dot plot Alignment

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

ENm006 - AF olfactory receptor family pseudogene

ENm006 - RP11-143H17.1 HAVANA pseudo Frameshift

ENm007 - AC HAVANA LIR pseudogene

ENm008 - Z HAVANA hemoglobin, alpha pseudogene

ENm009 - AC olfactory receptor, family 51, subfamily N, member 1 pseudogene Frameshift

ENm009 - AC olfactory receptor, family 52, subfamily Y, member 1 pseudogene

ENm009 - AC olfactory receptor, family 52, subfamily Z, member 1 pseudogene No Met First possible Met

ENm009 - AC olfactory receptor, family 51, subfamily A, member 10 pseudogene Frameshift

ENm009 - AC Novel pseudogene

ENm013 - AC ribosomal protein L5 (RPL5) pseudogene

ENr121 - AC hydroxytryptamine (serotonin) receptor 5B (HTR5B) pseudogene Frameshift

ENr131 - AC UDP glycosyltransferase 1 family, polypeptide A2 pseudogene Frameshift

ENr233 - AC Novel pseudogene 3’ truncation ~350aa missing, no stop

ENr233 - AC stereocilin (STRC) pseudogene Stop codon in exon 20

ENr322 - AL pseudogene similar to part of ribosomal protein L3 (RPL3) Protein dot plot mRNA dot plot

HAVANA pseudogene overlaps exon Non-coding locus –AC , AC , AC , AC , AC , AC , AC , AC , RP3-477O4.5 Coding locus opposite strand –AC , RP11-143H17.1, AC , RP11-398K22.9, RP3-477O4.4 Coding locus same strand –AC , Z , AC We believe all these pseudogenes are valid

Non-coding locus HAVANA sialyltransferase pseudogene Putative novel transcript Supporting EST Aligned proteins (column collapsed)

Coding locus opposite strand Protein alignment HAVANA novel pseudogene Non-coding exon ENm001 Pseudogene: AC

Coding locus same strand Frameshift LILRA3 LILR pseudogene

But not…. In-frame stop codon KIR2DL3 – coding gene