Human Transcriptome Annotations?

Question

[Bio_X2Y]

I am aware of only two full-scale off-the-shelf human transcriptome annotations:

• UCSC Known Genes
• ENSEMBL

Are there other significant ones?

EDIT 1: I've removed the second part of the question, as it was distracting.

EDIT 2: When I say "full-scale annotation", I mean an annotation that aims to comprehensively include all transcripts for which evidence exists.

For example, I wouldn't consider RefSeq to be a full-scale transcriptome annotation for two reasons:

• RefSeq itself is not an annotation - it is a set of curated sequences. (UCSC maps these to the genome for convenience, and this mapping could be considered a transcriptome annotation).
• RefSeq, by design, only represents a well-curated subset of the large number of transcripts for which evidence exists, so I wouldn't yet count it as "full-scale".

I consider UCSC Known Genes to be full-scale in the sense that it makes an attempt to comprehensively annotate all transcripts for which evidence exists. For this, it adopts evidence from a wide-range of sources, including RefSeq.

Thanks!

Answer 1

[Sean Davis]

For human, add to that list CCDS and RefSeq. If you go the UCSC genome browser, you will see that there are several others.

[Bio_X2Y]

Thanks Sean. I wouldn't consider RefSeq, etc., to be full-scale annotations - see clarification above.