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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| GRC Patch Release |
| GRCm38 patch release 4, alternate sequences and reference sequence patches |
| 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 |
| 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 () |
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UCSC Genes |
| UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics) |
| GENCODE (Ensembl)... |
| GENCODE Gene Annotations (Ensembl) |
| All GENCODE VM16 |
| All GENCODE annotations from VM16 (Ensembl 91) |
| All GENCODE VM14 |
| All GENCODE annotations from VM14 (Ensembl 89) |
| GENCODE VM11 (Ensembl 86) |
| Gene Annotations from ENCODE/GENCODE Version M11 (Ensembl 86) |
| GENCODE VM9 (Ensembl 84) |
| Gene Annotations from ENCODE/GENCODE Version M9 (Ensembl 84) |
| NCBI RefSeq |
| RefSeq gene predictions from NCBI |
| Other RefSeq |
| Non-Mouse RefSeq Genes |
| RetroGenes V6 |
| Retroposed Genes V6, Including Pseudogenes |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| CCDS |
| Consensus CDS |
| 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) |
| Geneid Genes |
| Geneid Gene Predictions |
| Genscan Genes |
| Genscan Gene Predictions |
| MGC Genes |
| Mammalian Gene Collection Full ORF mRNAs |
| Old UCSC Genes |
| Previous Version of UCSC Genes |
| ORFeome Clones |
| ORFeome Collaboration Gene Clones |
| Pfam in UCSC Gene |
| Pfam Domains in UCSC Genes |
| SGP Genes |
| SGP Gene Predictions Using Mouse/Human Homology |
| 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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| Mouse mRNAs |
| Mouse mRNAs from GenBank |
| Spliced ESTs |
| Mouse ESTs That Have Been Spliced |
| 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) |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
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FaceBase 24STypes |
| FaceBase 24 Sample Types Averaged |
| ORegAnno |
| Regulatory elements from ORegAnno |
| qPCR Primers |
| Mouse (mm10) Whole Transcriptome qPCR Primers |
| RefSeq Func Elems |
| NCBI RefSeq Functional Elements |
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| Conservation |
| Vertebrate Multiz Alignment & Conservation (60 Species) |
| 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 |
| Bonobo Chain/Net |
| Bonobo (Aug. 2015 (MPI-EVA panpan1.1/panPan2)), Chain and Net Alignments |
| Malayan flying lemur Chain/Net |
| Malayan flying lemur (Jun. 2014 (G_variegatus-3.0.2/galVar1)), Chain and Net Alignments |
| Chinese hamster Chain/Net |
| Chinese hamster (Aug. 2011 (CHO K1 cell line/criGriChoV1)), Chain and Net Alignments |
| Chimp Chain/Net |
| Chimp (Feb. 2011 (CSAC 2.1.4/panTro4)), Chain and Net Alignments |
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| Common SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples |
| RepeatMasker Viz. |
| Detailed Visualization of RepeatMasker Annotations |
| RepeatMasker |
| Repeating Elements by RepeatMasker |
| All SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) |
| All SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) |
| All SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) |
| Alternate strains... |
| Alternate mouse strain sequences |
| Alignment |
| Alternate mouse strains, alignments to reference genome |
| Alternate strains |
| Alternate mouse strains, mapped to their corresponding reference genome location |
| Common SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples |
| Common SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples |
| 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 |
| Mult. SNPs(142) |
| Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci |
| Mult. SNPs(138) |
| Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci |
| Mult. SNPs(137) |
| Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci |
| 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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