07c2860f23ceef6fd2952c5e0d10bd817dbe67f2 gperez2 Tue Aug 15 10:24:28 2023 -0700 Updating the FAQ on mitochondrial annotations for gene tracks, refs #19880 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index d45f60d..0b0cbb1 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -410,32 +410,34 @@ special and most of what has been explained on this page does not apply to the mitochondrial gene annotations. For most assemblies in the Genome Browser, the sequence name of the mitochondrial genome is "chrM".<p> <p> For hg19, no mitochondrial genome was originally published. The UCSC Genome Browser added a chrM sequence that was not the mitochondrial genome sequence later selected by NCBI for GRCh37. This is why <strong>the current hg19 version contains two mitochondrial sequences, the old one called "chrM" and the current GRCh37 reference, called "chrMT"</strong>. The issue is described in detail in our <a target=_blank href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/README.txt"> hg19 sequence download instructions</a>. If you use hg19 today, chrMT should be considered the current mitochondrial sequence, chrM is only supported for backwards compatibility and legacy annotation files. <p> -For chrM or chrMT (on hg19), the GENCODE tracks contain the same gene -annotations, but RefSeq annotations only exist on chrM. Both databases +For hg38, the GENCODE and ClinVar variants annotations are all present on chrM. The RefSeq Other +Annotations data is not made by the RefSeq group and annotations are on chrM. For hg19, legacy +annotations such as the UCSC Genes are on chrM. All more recent annotations, the RefSeq Other +Annotations and NCBI ClinVar variants are on chrMT. Both GENCODE and RefSeq databases import their mitochondrial gene annotation directly from the rCRS RefSeq record <a target=_blank href="https://www.ncbi.nlm.nih.gov/nuccore/251831106">NC_012920.1</a>. The annotation was provided by <a target=_blank href="https://www.mitomap.org/MITOMAP">Mitomap.org</a>, which provides detailed documentation about the <a href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoSeqs" target=_blank>the history of this sequence</a>. <a name="report"></a> <h2>How shall I report a gene transcript in a manuscript?</h2> <p> When reporting on GENCODE/Ensembl transcripts, please specify the ENST