HAVANA_ID ENCODE_ID Reason for assignment as pseudogene AC006326.4-001 Contains disablement(s)^1 AC006326.2-001 Fragment - contains disablement(s)^1 AC063976.2-001 Contains disablement(s) RP1-127L4.3-001 Fragment - contains frameshift - exon order changed^2 AF277315.12-001 Contains disablement(s)^3 RP11-143H17.1-001 Contains disablement(s) AC009892.5-001 Contains disablement(s) Z84721.2-001 Contains disablement(s)^4 Z84721.4-001 Contains disablement(s) AC103710.2-001 Contains disablement(s)^5 AC103710.4-001 Contains disablement(s)^6 AC129505.5-001 Contains disablement(s)^7 AC087380.10-001 Contains disablement(s)^5 AC087380.14-001 Contains disablement(s) AC002456.1-001 Fragment^8 AC009404.5-001 Contains disablement(s) AC114812.7-001 Contains disablement(s) AC011330.5-001 Truncation^9 AC011330.8-001 Contains disablement(s) AL162151.3-001 Fragment^10 1 – mitochondrial protein pseudogene - probably missed as internal to HNRPA1 pseudogene 2 – exon order changed compared to “companion” pseudogene RP1-127L4.2-001 – ie 3’ exon of two is found furthest upstream– presumably originated from the same duplication and subsequently rearranged 3 – OR pseudogene - weak protein homology 4 – HBZ pseudogene – there is a single in frame stop codon at position 7 and another ATG at position 14 which could reconstitute an ORF – however, there is no transcript evidence with best in genome alignment to the first coding exon 5 – OR receptor – frameshift leads to small C-terminal truncation which compromises TM domain 7 (TM7) 6 – OR receptor – weak protein homology – LINE element inserted into pseudogene 7 – OR receptor – conserved ATG missing – next available ATG lies in TM1 and would likely lead to structural problems 8 – N- and C-terminal truncated but contains no disablements – no evidence to support transcription 9 - 10 – presumed single retrotransposition event has been rearranged so N- and C-terminal fragments appear adjacent to one another but on different strands – neither part contains disablements