Control track and group visibility more selectively below.
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| 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 |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| Short Match |
| Perfect Matches to Short Sequence (CAGCAGCAGCAGCAGCAGCAGCAGCAG...) |
| Tandem Dups |
| Paired identical sequences |
| UCSC liftOver mm10 |
| UCSC liftOver alignments to mm10 |
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| updated
GENCODE VM36 |
| GENCODE VM36 |
| NCBI RefSeq |
| RefSeq genes from NCBI |
| updated
GENCODE Versions |
| Container of all new and previous GENCODE releases |
| All GENCODE VM26 |
| All GENCODE annotations from VM26 (Ensembl 103) |
| All GENCODE VM27 |
| All GENCODE annotations from VM27 (Ensembl 104) |
| All GENCODE VM28 |
| All GENCODE annotations from VM28 (Ensembl 105) |
| All GENCODE VM29 |
| All GENCODE annotations from VM29 (Ensembl 106) |
| All GENCODE VM30 |
| All GENCODE annotations from VM30 (Ensembl 107) |
| All GENCODE VM31 |
| All GENCODE annotations from VM31 (Ensembl 108) |
| All GENCODE VM32 |
| All GENCODE annotations from VM32 (Ensembl 109) |
| All GENCODE VM33 |
| All GENCODE annotations from VM33 (Ensembl 110) |
| All GENCODE VM34 |
| All GENCODE annotations from VM34 (Ensembl 111) |
| All GENCODE VM35 |
| All GENCODE annotations from VM35 (Ensembl 112) |
| new
All GENCODE VM36 |
| All GENCODE annotations from VM36 (Ensembl 113) |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| CRISPR Targets |
| CRISPR/Cas9 -NGG Targets, whole genome |
| GENCODE Archive |
| GENCODE Archive |
| GENCODE VM35 |
| GENCODE VM35 |
| GENCODE VM33 |
| GENCODE VM33 |
| GENCODE VM32 |
| GENCODE VM32 |
| GENCODE VM30 |
| GENCODE VM30 |
| GENCODE VM27 |
| GENCODE VM27 |
| Genscan Genes |
| Genscan Gene Predictions |
| Other RefSeq |
| Non-Mouse RefSeq Genes |
| Pfam in UCSC Gene |
| Pfam Domains in UCSC Genes |
| TOGA vs. hg38 |
| TOGA annotations using human/hg38 as reference |
| UCSC Alt Events |
| Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes |
| UniProt |
| UniProt SwissProt/TrEMBL Protein Annotations |
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| RefSeq mRNAs |
| RefSeq mRNAs mapped to this assembly |
| Mouse mRNAs |
| Mouse mRNAs from GenBank |
| Mouse ESTs |
| Mouse ESTs Including Unspliced |
| Other mRNAs |
| Non-Mouse mRNAs from GenBank |
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| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| JASPAR Transcription Factors |
| JASPAR Transcription Factor Binding Site Database |
| ReMap ChIP-seq |
| ReMap Atlas of Regulatory Regions |
| VISTA Enhancers |
| VISTA Enhancers |
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| Conservation |
| Vertebrate Multiz Alignment & Conservation (35 Species) |
| Chain/Net |
| Chain and Net Alignments |
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| RepeatMasker |
| Repeating Elements by RepeatMasker |
| 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 |
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