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Configure Tracks on UCSC Genome Browser: Chicken Mar. 2018 (GRCg6a/galGal6)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   MethBase2    
Chicken methylome studies Chicken methylome studies
     SRP295626     WGBS of liver for chicken with fatty liver [Liver]
     SRP252164     The dynamic methylome of the broiler chicken as a resource for livestock performance biomarker development [Breast, Ileum, Jejunum, Spleen]
     SRP235124     Evolution of CpH methylation in vertebrate brains [Brain, Cortex, Forebrain]
     SRP233032     Whole-genome bisulfite sequencing of hypothalamus and ovary in Langshan chicken [Hypothalamus, Ovary]
     SRP188450     A homeostasis hypothesis of avian influenza resistance in chickens [Lung]
     SRP041344     Single-base resolution DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, by whole-genome bisulfite sequencing (MethylC-seq). [Lung]
     SRP041054     Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes [Sperm]
     SRP028242     Gallus gallus Epigenomics
     SRP033603     Gallus gallus transcriptome [Embryo]
     SRP108572     Whole genome DNA methylation sequencing of the chicken retina, cornea and brain [Brain, Cornea, Retina]
     SRP504622     Influence of DNA-methylation at multiple stages of limb chondrogenesis [Hindlimb 28HH third interdigit]
     SRP092806     Gallus gallus Epigenomics [Breast Muscle]
     SRP466458     Gallus gallus strain:blue eggshell strain | breed:Xuefeng Black-bone chicken Raw sequence reads [Shell Gland]
     SRP464968     WGBS for chicken myoblast DM_vs_GM [Leg Muscle]
     SRP430459     WGBS of chicken embryonic gonads between sexes [Gonad]
     SRP426826     Sequencing of DNA methylation in chicken adipose tissue [Adipose Tissue]
     SRP387729     Genome-wide DNA methylation landscape of spleens from chickens with different resistance to infection with Marek's disease [Spleen]
     SRP359458     Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation [Bisulfite-seq] [Lens Epithelial, Lens Fiber]
     SRP321573     Conservation and divergence of DNA methylation patterns and functions in vertebrates [Primary Dermal Fibroblasts, Psoas Muscle]
     SRP309852     Gallus gallus strain:chicken Raw sequence reads [Mandibular Condyle]
     SRP304961     Gallus gallus Raw sequence reads [Leg Muscle]
     SRP304425     Whole-genome bisulfite sequencing of Chinese indigenous chicken resources [Blood]
     ERP126680     GENE-SWITCH Chicken DNA methylation with Whole Genome bisulfite sequencing (WGBS) [AIL Embryo E8 pool3 hindlimb muscle, AIL Embryo E8 pool3 skin, AIL Embryo E8 pool3 small intestine, AIL Embryo E8 pool4 hindbrain, AIL Embryo E8 pool4 kidney, AIL Embryo E8 pool4 liver, AIL Embryo E8 pool4 lung, Cerebellum, Hindlimb Muscle, Kidney, Liver, Lung, Skin Of Back, Small Intestine]
     ERP144515     FAANG Chicken SL-29 cell line
     Common     Common methbase tracks for the galGal6 assembly
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Assembly Assembly from Fragments
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
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 ()
-   Genes and Gene Predictions    
NCBI RefSeq RefSeq gene predictions from NCBI
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CRISPR 10K CRISPR/Cas9 Sp. Pyog. target sites (exons +/- 10,000 bp)
     CRISPR Regions 10K     Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 10,000 bp)
     CRISPR Targets 10K     CRISPR/Cas9 -NGG Targets (exons +/- 10,000 bp)
Ensembl Genes Ensembl Genes
Genscan Genes Genscan Gene Predictions
Other RefSeq Non-Chicken RefSeq Genes
TransMap V5 TransMap Alignments Version 5
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   mRNA and EST    
Chicken ESTs Chicken ESTs Including Unspliced
Chicken mRNAs Chicken mRNAs from GenBank
Other mRNAs Non-Chicken mRNAs from GenBank
Spliced ESTs Chicken 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    
Conservation Vertebrate Multiz Alignment & Conservation (77 Species)
Birds Chain/Net Birds Chain and Net Alignments
Fish Chain/Net Fish Chain and Net Alignments
Vertebrate Chain/Net Vertebrate Chain and Net Alignments
Chicken Chain/Net Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)), Chain and Net Alignments
Mouse Chain/Net Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments
-   Variation and Repeats    
RepeatMasker Repeating Elements by RepeatMasker
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