yep, looks like that's the problem I wonder why it doesn't have a CDS chromosome in ENSEMBL? That's a bit nuts.
It is indeed indexed to MT in the canonical ENSEMBL database: https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000198727;r=MT:14747-15887;t=ENST00000361789 --t On Thu, Mar 28, 2024 at 9:59 AM Vincent Carey <st...@channing.harvard.edu> wrote: > winging it here tim > > > select(Homo.sapiens, keys="ENSG00000198727", keytype="ENSEMBL", > columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) > 'select()' returned 1:1 mapping between keys and columns > ENSEMBL GENENAME SYMBOL CDSCHROM GENEID > 1 ENSG00000198727 cytochrome b CYTB <NA> 4519 > > select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL", > columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) > 'select()' returned 1:1 mapping between keys and columns > SYMBOL GENENAME CDSCHROM GENEID > 1 MTCYBP1 MT-CYB pseudogene 1 <NA> 100499418 > > relevant? > > On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. <tim.tri...@gmail.com> > wrote: > >> Hi Lori and fellow maintainers, >> >> I had a strange experience yesterday where I pulled down genes and >> transcripts from Homo.sapiens, only to discover that all mitochondrial >> encoded genes (MT-CYB, MT-CO2, etc) were missing. >> >> Is there an historical reason why this is so? Obviously these transcripts >> are physiologically important, but beyond that, they’re also used all the >> time in single cell sequencing to estimate viability. >> >> Best, >> >> --t >> >> > On Mar 28, 2024, at 8:47 AM, Kern, Lori via Bioc-devel < >> bioc-devel@r-project.org> wrote: >> > >> > Hello Bioconductor community, >> > >> > The newest db0, OrgDb, and TxDb annotation packages for the upcoming >> Bioconductor 3.19 release are up and available for download in the devel >> version of Bioconductor. >> > >> > The deadline for submitting contributed annotation packages will be >> Wednesday April 17 th. >> > >> > The new db0 packages are: >> > >> > anopheles.db0_3.19.0.tar.gz >> > arabidopsis.db0_3.19.0.tar.gz >> > bovine.db0_3.19.0.tar.gz >> > canine.db0_3.19.0.tar.gz >> > chicken.db0_3.19.0.tar.gz >> > chimp.db0_3.19.0.tar.gz >> > ecoliK12.db0_3.19.0.tar.gz >> > ecoliSakai.db0_3.19.0.tar.gz >> > fly.db0_3.19.0.tar.gz >> > human.db0_3.19.0.tar.gz >> > malaria.db0_3.19.0.tar.gz >> > mouse.db0_3.19.0.tar.gz >> > pig.db0_3.19.0.tar.gz >> > rat.db0_3.19.0.tar.gz >> > rhesus.db0_3.19.0.tar.gz >> > worm.db0_3.19.0.tar.gz >> > xenopus.db0_3.19.0.tar.gz >> > yeast.db0_3.19.0.tar.gz >> > zebrafish.db0_3.19.0.tar.gz >> > >> > The new OrgDb packages are: >> > >> > GO.db_3.19.0.tar.gz >> > org.Ag.eg.db_3.19.0.tar.gz >> > org.At.tair.db_3.19.0.tar.gz >> > org.Bt.eg.db_3.19.0.tar.gz >> > org.Ce.eg.db_3.19.0.tar.gz >> > org.Cf.eg.db_3.19.0.tar.gz >> > org.Dm.eg.db_3.19.0.tar.gz >> > org.Dr.eg.db_3.19.0.tar.gz >> > org.EcK12.eg.db_3.19.0.tar.gz >> > org.EcSakai.eg.db_3.19.0.tar.gz >> > org.Gg.eg.db_3.19.0.tar.gz >> > org.Hs.eg.db_3.19.0.tar.gz >> > org.Mm.eg.db_3.19.0.tar.gz >> > org.Mmu.eg.db_3.19.0.tar.gz >> > org.Pt.eg.db_3.19.0.tar.gz >> > org.Rn.eg.db_3.19.0.tar.gz >> > org.Sc.eg.db_3.19.0.tar.gz >> > org.Ss.eg.db_3.19.0.tar.gz >> > org.Xl.eg.db_3.19.0.tar.gz >> > Orthology.eg.db_3.19.0.tar.gz >> > PFAM.db_3.19.0.tar.gz >> > >> > The new TxDb packages are: >> > >> > TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz >> > TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz >> > >> > Thank you >> > >> > >> > Lori Shepherd - Kern >> > >> > Bioconductor Core Team >> > >> > Roswell Park Comprehensive Cancer Center >> > >> > Department of Biostatistics & Bioinformatics >> > >> > Elm & Carlton Streets >> > >> > Buffalo, New York 14263 >> > >> > >> > This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > The information in this email is intended only for the...{{dropped:11}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel