cb5adc121fe56896ad3167b96f150ce3a5fa973c dschmelt Thu Jul 9 12:11:31 2020 -0700 Slight modifications to Max's new mitochondria FAQ #25845 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 01c7961..1d86cb9 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -337,46 +337,56 @@ for either NCBI or BLAT to get the correct alignment and gene model because the genome sequence is missing for part of the gene. NCBI and BLAT find slightly different exon boundaries at the edge of the problematic region. NCBI's aligner tries very hard to find exons that align to any transcript sequence, so it calls a few small dubious "exons" in the affected genomic region. GENCODE V19 also used an aligner that tried very hard to find exons, but it found small dubious "exons" in different places than NCBI. The <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite">RefSeq Alignments</a> subtrack makes the problematic region very clear with double lines indicating unalignable transcript sequence. </p> <a name="mito"></a> <h2>What is the best gene track for mitochondrial gene annotations</h2> <p> -The mitochondrial sequence included in assembly sequence files is a very -special genome and most of what has been explained on this page does not apply +The mitochondrial sequence included in assembly sequence files is very +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> -Sidenote: if you use hg19, note that hg19 in the UCSC Genome Browser had a chrM sequence -that was not the mitochondrial genome sequence selected by NCBI later for GRCh37. This -is why the current hg19 version of the Genome Browser contains two mitochondrial sequences, -the old one called "chrM" and the one that is part of the GRCh37 reference, called "chrMT". The issue -is described in detail in our <a target=_blank href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/README.txt"> -hg19 Download instructions</a>. If you use hg19 today, chrMT should be -considered the mitochondrial genome, chrM is only supported for backwards +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 NCBI RefSeq or Ensembl/Gencode tracks contain the same gene annotations. -Both 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>. +For chrM or chrMT (on hg19), the GENCODE tracks contain the same gene +annotations, but RefSeq annotations only exist on chrM. Both 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 identifier. It is often helpful to also specify the Ensembl release, which is shown on the details page, when you click onto a transcript. </p> <p> When reporting RefSeq transcripts, e.g. in HGVS, prefer the "NCBI RefSeq" track over the "UCSC RefSeq track". Please specify the RefSeq transcript ID and also the RefSeq annotation release.