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    Chromosome 1: 2,000,001-3,000,000

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    Assembly exceptions

    GRC assembly patches, haplotype (HAPs) and pseudo autosomal regions (PARs)

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    Assembly exceptions

    GRC assembly patches, haplotype (HAPs) and pseudo autosomal regions (PARs)

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    Region in detail

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    Basic Gene Annotations from GENCODE 19

    The GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).

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    Sequence

    Track showing sequence in both directions. Only displayed at 1Kb and below.

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    Human cDNAs (RefSeq)

    Human cDNAs from NCBI RefSeq are aligned to the genome using GeneWise.

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    Assembly exceptions

    GRC assembly patches, haplotype (HAPs) and pseudo autosomal regions (PARs)

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    Sequence

    Track showing sequence in both directions. Only displayed at 1Kb and below.

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    Human cDNAs (RefSeq)

    Human cDNAs from NCBI RefSeq are aligned to the genome using GeneWise.

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    Primary assembly mapping

    Mappings between primary assembly and alternate loci or patches.

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    Assembly exceptions

    GRC assembly patches, haplotype (HAPs) and pseudo autosomal regions (PARs)

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    Basic Gene Annotations from GENCODE 19

    The GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).

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    Add/remove tracksCustom tracksResize imageExport imageReset configurationReset track order

    Chromosome bands

    Cytogenetic bands

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    Age of Base

    Timing of the most recent mutation as determined by inter-species whole genome alignments. Each base pair in which the human reference genome differs by substitution from one of its inferred ancestral genomes is colored in either grey (event prior to the primate branch), blue (primate specific), red (human specific, fixed variant), or yellow (human specific segregating variant, i.e. SNP). Clicking on a mutation position reveals the sub-tree of species which have inherited the same mutation from their common ancestor. It also reveals a score that represents the age of the mutation in arbitrary units, and determines the intensity of the coloring. The more recent the mutation, the lower the score and the darker the color.

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    EST cluster (Unigene)

    Positions of UniGene sequences along the genome. These are determined using TBLASTN of Genscan predictions against UniGene sequences.

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    CCDS set

    Protein coding sequences agreed upon by the Consensus Coding Sequence project, or CCDS.

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    Contigs

    Track showing underlying assembly contigs.

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    CCDS set

    Protein coding sequences agreed upon by the Consensus Coding Sequence project, or CCDS.

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    EST cluster (Unigene)

    Positions of UniGene sequences along the genome. These are determined using TBLASTN of Genscan predictions against UniGene sequences.

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    All phenotype-associated - short variants (SNPs and indels)

    Variants that have been associated with a phenotype or a disease

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    1000 Genomes 3 - All (structural variants)

    Variants genotyped by the 1000 Genomes project (phase 3)

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    Regulatory features

    Features from Ensembl Regulatory Build.

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    Age of Base

    Timing of the most recent mutation as determined by inter-species whole genome alignments. Each base pair in which the human reference genome differs by substitution from one of its inferred ancestral genomes is colored in either grey (event prior to the primate branch), blue (primate specific), red (human specific, fixed variant), or yellow (human specific segregating variant, i.e. SNP). Clicking on a mutation position reveals the sub-tree of species which have inherited the same mutation from their common ancestor. It also reveals a score that represents the age of the mutation in arbitrary units, and determines the intensity of the coloring. The more recent the mutation, the lower the score and the darker the color.

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