GENCODE v2.2 Known problems

If you've found a problem that is not listed here, please report it to Julien Lagarde (jlagardeatimim.es) and/or France Denoeud (fdenoeudatimim.es).

->The coding transcripts for which a 'start_codon' gtf record is missing have a WRONG GTF FRAME ATTRIBUTE!

->RP3-477O4.2-001's 4th CDS exon is shorter than in previous release, which introduces in frame stops

->AP000313.6-002's CDS record includes stop codon

->AC069356.3-002 has one in-frame stop, although it is annotated as coding.

->AC011501.5-006: the 'start_codon' is misannotated and is in fact somewhere upstream (HAVANA didn't find it)

->The six following transcripts have CDS nucleotide sequence lengths that are not a multiple of 3 (reported to Havana):
- AP000280.67-002
- AF277315.16-006
- RP11-115M6.1-005
- AC006153.2-013
- RP11-505P4.2-015
- AP001462.3-013
-> all 6 AA seqs end with X except last one with A (unambiguous 'GC-' triplet)

->Locus XX-FW81657B9.1 (GDI1) partially overlaps the gap in ENm006
A part of it was annotated in June release: chrX:153234162-153235518, but removed from October release