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Configure Tracks on UCSC Genome Browser: Rhesus Feb. 2019 (Mmul_10/rheMac10)
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-   MethBase2    
Rhesus methylome studies Rhesus methylome studies
     SRP265909     Whole genome bisulfite sequencing from primate brains (orthologous region to human BA46) [Brain]
     SRP049936     DNA methylation in mammalian placentas [Cerebrum, Cord Blood, Extraembryonic Membrane, Placenta, Trophoblasts]
     SRP241850     WGBS of Chinese rhesus macaque peripheral blood [Blood]
     SRP220230     Human, Chimpanzee, Gorilla, Orangutan, Macaque Epigenomics [LCL]
     SRP045312     Wax and Wane of genome-wide DNA methylation during monkey preimplantation embryogenesis [Gamete]
     SRP136499     A genomic study of the contribution of DNA methylation to regulatory evolution in primates [Heart, Heart (Later Reclassified As Liver), Kidney, Liver, Lung]
     SRP149295     Epigenetic maintenance of topological domains in the rearranged gibbon genome [WBGS] [White Blood]
     SRP131117     Reprogramming of meiotic chromatin architecture during primate spermatogenesis [Pachytene Spermatocyte, Round Spermatid, Sperm, Spermatogonia]
     SRP417565     A somatic cell cloned rhesus monkey obtained by trophoblast replacement [WGBS I] [In Vitro Cultured Embryos, Placenta]
     SRP412039     Whole Genome Bisulfite Sequencing of Rhesus Sperm Exposed to THC [Sperm]
     SRP405758     Comparative analysis of epigenomic evolution in mammals [Liver, Skeletal Muscle]
     SRP390347     Macaca mulatta Epigenomics [Thymus]
     SRP068766     Comparative Methylome Analyses Reveal Human Brain Specific Methylated Regions Implicated in Transcription Regulation [Brain]
     SRP009594     Dramatic effects of social behavior on gene regulation in rhesus macaques [Bisulfite seq] [PBMC]
     SRP286979     Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta [Cerebellum, Cortex, Embryo, Fibroblast, Heart, Kidney, Liver, Placenta, Small Intestine]
     SRP312597     Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models [Cortex, Hippocampus, Hypothalamus, cffDNA]
     ERP139499     Whole genome bisulfite sequencing of liver samples of five mammals (human, rhesus macaque, mouse, rat and dog) [Liver]
     Common     Common methbase tracks for the rheMac10 assembly
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Gap Gap Locations
Assembly Assembly from Fragments
GC Percent GC Percent in 5-Base Windows
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
Tandem Dups Paired identical sequences
-   Genes and Gene Predictions    
NCBI RefSeq RefSeq genes from NCBI
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
Ensembl Genes Ensembl Genes
Genscan Genes Genscan Gene Predictions
Other RefSeq Non-Rhesus RefSeq Genes
TOGA vs. hg38 TOGA annotations using human/hg38 as reference
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   mRNA and EST    
Rhesus ESTs Rhesus ESTs Including Unspliced
Rhesus mRNAs Rhesus mRNAs from GenBank
Spliced ESTs Rhesus ESTs That Have Been Spliced
-   Expression and Regulation    
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
-   Comparative Genomics    
ClinVar Lift Human ClinVar variants lifted to Rhesus
hg19 ChainNet Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments
Human Chain/Net Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments
mm10 ChainNet Mouse (Dec. 2011 (GRCm38/mm10)), Chain and Net Alignments
Mouse Chain/Net Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments
Hawaiian monk seal Chain/Net Hawaiian monk seal (Jun. 2017 (ASM220157v1/neoSch1)), Chain and Net Alignments
-   Variation and Repeats    
RepeatMasker Repeating Elements by RepeatMasker
Rhesus SNVs Annotated SNVs from the Rhesus Macaque Sequencing Consortium
updated EVA SNP Short Genetic Variants from European Variant Archive
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust