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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| All Gaps |
| All gaps of unknown nucleotides (N's), including AGP annotated gaps |
| Assembly |
| Assembly from Fragments |
| Chromosome Band |
| Chromosome Bands Based On Microscopy |
| Clone Ends |
| Mapping of clone libraries end placements |
| Contigs |
| Contig fragments used in the assembly |
| Gap |
| Gap Locations |
| GC Percent |
| GC Percent in 5-Base Windows |
| GRC Incident |
| GRC Incident Database |
| p14
GRC Patches |
| GRC Patches: Alt Haplotypes and Fix Sequences |
| INSDC |
| Accession at INSDC - International Nucleotide Sequence Database Collaboration |
MGI QTL |
| Mouse Genome Informatics Quantitative Trait Loci ***Lifted from NCBI 37 (mm9)*** |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| Short Match |
| Perfect Matches to Short Sequence () |
| UCSC liftOver mm39 |
| UCSC liftOver alignments to mm39 |
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| GENCODE VM23 |
| GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default) |
| NCBI RefSeq |
| RefSeq genes from NCBI |
| GENCODE Versions |
| Container of all new and previous GENCODE releases |
| GENCODE VM9 (Ensembl 84) |
| Gene Annotations from ENCODE/GENCODE Version M9 (Ensembl 84) |
| GENCODE VM11 (Ensembl 86) |
| Gene Annotations from ENCODE/GENCODE Version M11 (Ensembl 86) |
| All GENCODE VM14 |
| All GENCODE annotations from VM14 (Ensembl 89) |
| All GENCODE VM16 |
| All GENCODE annotations from VM16 (Ensembl 91) |
| All GENCODE VM18 |
| All GENCODE annotations from VM18 (Ensembl 93) |
| All GENCODE VM22 |
| All GENCODE annotations from VM22 (Ensembl 97) |
| All GENCODE VM24 |
| All GENCODE annotations from VM24 (Ensembl 99) |
| All GENCODE VM25 |
| All GENCODE annotations from VM25 (Ensembl 100) |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| CCDS |
| Consensus CDS |
| CRISPR 10K |
| CRISPR/Cas9 Sp. Pyog. target sites (exons +/- 10,000 bp) |
| CRISPR Targets 10K |
| CRISPR/Cas9 -NGG Targets (exons +/- 10,000 bp) |
| CRISPR Regions 10K |
| Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 10,000 bp) |
| CRISPR Targets |
| CRISPR/Cas9 -NGG Targets, whole genome |
| Geneid Genes |
| Geneid Gene Predictions |
| Genscan Genes |
| Genscan Gene Predictions |
| MGC/ORFeome Genes |
| MGC/ORFeome Full ORF mRNA Clones |
| ORFeome Clones |
| ORFeome Collaboration Gene Clones |
| MGC Genes |
| Mammalian Gene Collection Full ORF mRNAs |
| Old UCSC Genes |
| Previous Version of UCSC Genes |
| Other RefSeq |
| Non-Mouse RefSeq Genes |
| Pfam in UCSC Gene |
| Pfam Domains in UCSC Genes |
| RetroGenes V6 |
| Retroposed Genes V6, Including Pseudogenes |
| SGP Genes |
| SGP Gene Predictions Using Mouse/Human Homology |
| TOGA vs. hg38 |
| TOGA annotations using human/hg38 as reference |
| TransMap V5 |
| TransMap Alignments Version 5 |
| TransMap ESTs |
| TransMap EST Mappings Version 5 |
| TransMap RNA |
| TransMap GenBank RNA Mappings Version 5 |
| TransMap RefGene |
| TransMap RefSeq Gene Mappings Version 5 |
| TransMap Ensembl |
| TransMap Ensembl and GENCODE Mappings Version 5 |
| tRNA Genes |
| Transfer RNA Genes Identified with tRNAscan-SE |
| UCSC Alt Events |
| Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes |
| UniProt |
| UniProt SwissProt/TrEMBL Protein Annotations |
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| Lens Patents |
| Lens PatSeq Patent Document Sequences |
| UniProt Variants |
| UniProt/SwissProt Amino Acid Substitutions |
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| Spliced ESTs |
| Mouse ESTs That Have Been Spliced |
| Mouse ESTs |
| Mouse ESTs Including Unspliced |
| Mouse mRNAs |
| Mouse mRNAs from GenBank |
| Other mRNAs |
| Non-Mouse mRNAs from GenBank |
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| ENCODE cCREs |
| ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types |
| Tabula Muris |
| Single Cell FACS RNA-Seq of 44,779 cells from Tabula Muris |
| Splice Sites |
| Tabula Muris single cell RNA-Seq splice sites |
| Genome Coverage |
| Tabula Muris single cell RNA-Seq genome coverage |
| Cell expression |
| Single Cell RNA-Seq Gene Expression from Tabula Muris |
| 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) |
| ENC+EPD Enhc-Gene |
| Enhancer-gene map from ENCODE 3 (UCSD/Ren) with promoters from EPDnew |
| ENCODE Regulation |
| Integrated Regulation from ENCODE |
| Open Chromatin |
| Open chromatin in embryonic tissue (12 tissues, 8 ages) from ATAC-seq by ENCODE 3 (UCSD/Ren) |
| Histone Modifications |
| Histone modifications in embryonic tissue (8 marks, 12 tissues, 8 ages) from ChIP-seq by ENCODE 3 (UCSD/Ren) |
| Chromatin State |
| Chromatin state of embryonic tissue (12 tissues, 8 ages) from ENCODE 3 (UCSD/Ren) |
| EPDnew Promoters |
| Promoters from EPDnew |
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FaceBase 24STypes |
| FaceBase 24 Sample Types Averaged |
| FANTOM5 |
| FANTOM5: Mapped transcription start sites (TSS) and their usage |
| TSS activity (TPM) |
| TSS activity per sample (TPM) |
| TSS activity (read counts) |
| TSS activity per sample (read counts) |
| Max counts |
| Max counts of CAGE reads |
| Total counts |
| Total counts of CAGE reads |
| TSS peaks |
| FANTOM5: DPI peak, robust set |
| JASPAR Transcription Factors |
| JASPAR Transcription Factor Binding Site Database |
| ORegAnno |
| Regulatory elements from ORegAnno |
| qPCR Primers |
| Mouse (mm10) Whole Transcriptome qPCR Primers |
| RefSeq Func Elems |
| NCBI RefSeq Functional Elements |
| ReMap ChIP-seq |
| ReMap Atlas of Regulatory Regions |
| updated
VISTA Enhancers |
| VISTA Enhancers |
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| Conservation |
| Vertebrate Multiz Alignment & Conservation (60 Species) |
| ClinVar Lift |
| Human ClinVar variants lifted to Mouse |
| Euarch Chain/Net |
| Euarchontoglire Genomes, Chain and Net Alignments |
| Glires Chain/Net |
| Glires Genomes, Chain and Net Alignments |
| Placental Chain/Net |
| Placental Genomes, Chain and Net Alignments |
| Vertebrate Chain/Net |
| Vertebrate Genomes, Chain and Net Alignments |
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| Common SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples |
| RepeatMasker |
| Repeating Elements by RepeatMasker |
| Alternate strains |
| Alternate mouse strain sequences |
| Alternate strains |
| Alternate mouse strains, mapped to their corresponding reference genome location |
| Alignment |
| Alternate mouse strains, alignments to reference genome |
| Interrupted Rpts |
| Fragments of Interrupted Repeats Joined by RepeatMasker ID |
| Microsatellite |
| Microsatellites - Di-nucleotide and Tri-nucleotide Repeats |
| Mouse SNPs |
| Annotated SNPs from mouse strain comparison analysis |
| dbSNP Archive |
| dbSNP Track Archive |
| Mult. SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci |
| Common SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples |
| All SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) |
| Mult. SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci |
| Common SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples |
| All SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) |
| Mult. SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci |
| All SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) |
| EVA SNP |
| Short Genetic Variants from European Variant Archive |
| RepeatMasker Viz. |
| Detailed Visualization of RepeatMasker Annotations |
| Segmental Dups |
| Duplications of >1000 Bases of Non-RepeatMasked Sequence |
| Simple Repeats |
| Simple Tandem Repeats by TRF |
| WM + SDust |
| Genomic Intervals Masked by WindowMasker + SDust |
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