- Sequence
- No additional information available.
- CytoBands
- cytoband information from various sources (some manually)
- LINEs bp/Mb
- Sum of bases comprising LINE elements per Mb.
- SINEs bp/Mb
- Sum of bases comprising SINE elements per Mb.
- LTRs bp/Mb
- Sum of bases comprising LTR elements per Mb.
- RMSKs/Mb
- Sum of bases comprising RMSK elements per Mb.
- Polys/Mb
- count of SNPs/InDels/Diffs per Mb.
- Exons bp/Mb
- Sum of bases comprising unique refseq exons per Mb.
- miRNAs
- positional mapping of miRNA genes from miRBase (v9.0, Sanger)
- Assembly GAPs
- Assembly Gaps from Mapview Information
- Macaque GBSB
- Precursor Syntenic Block Predictions
- Mouse GBSB
- Precursor Syntenic Block Predictions
- Human GBSB
- Precursor Syntenic Block Predictions
- Cat GBSB
- Precursor Syntenic Block Predictions
- Horse GBSB
- Precursor Syntenic Block Predictions
- Dog GBSB
- Precursor Syntenic Block Predictions
- Rat GBSB
- Precursor Syntenic Block Predictions
- Chimp GBSB
- Precursor Syntenic Block Predictions
- Opossum GBSB
- Precursor Syntenic Block Predictions
- Assembly GAPs
- Assembly Gaps from Mapview Information
- miRNA Alignments
- positional mapping of miRNA genes from miRBase (v9.0, Sanger)
- nonB DNA Segments
- ABCC identified nonB DNA sequences from the Genomic sequence.
- Macaque GBSB
- Precursor Syntenic Block Predictions
- Mouse GBSB
- Precursor Syntenic Block Predictions
- Human GBSB
- Precursor Syntenic Block Predictions
- Cat GBSB
- Precursor Syntenic Block Predictions
- Horse GBSB
- Precursor Syntenic Block Predictions
- Dog GBSB
- Precursor Syntenic Block Predictions
- Chimp GBSB
- Precursor Syntenic Block Predictions
- Rat GBSB
- Precursor Syntenic Block Predictions
- opossum GBSB
- Precursor Syntenic Block Predictions
- MARC Markers
- No additional information available.
- ILTX_2005 Markers
- No additional information available.
- CytoGenes (NCBI)
- Genes Mapped to CytoGenetic Bands. Parsed from NCBI Mapview Information Extrapolating from ISCN Coordinates.
- GMapped STS Alignments (ABCC)
- Mouse-Specific STS Sequences from Genbank aligned using GMap
- STS Sequences (NCBI)
- STS Marker Sequences. Parsed from NCBI Mapview Information.
- Refseq Promoters (NCBI/ABCC)
- Refseq Promoter Regions (defined as -1500 --> +200 of transcription start site
- Refseq Genes (NCBI)
- No additional information available.
- Refseq mRNAs (NCBI)
- Refseq mRNAs
- Genscan mRNAs (ABCC)
- ABCC Genscan mRNAs.
- Genscan Genes (ABCC)
- ABCC Genscan Genes.
- Model mRNAs (NCBI)
- NCBI Model mRNAs. Parsed from NCBI Mapview Information
- Model Genes (NCBI)
- NCBI Model Genes. Parsed from NCBI Mapview Information
- DNA/GC content
- No additional information available.
- CpG Islands
- CpG Islands.
- Oligos
- ABCC identified Oligo sequences from the Genomic sequence.
- nonB DNA Segments
- ABCC identified nonB DNA sequences from the Genomic sequences.
- Rare RESites
- ABCC identified RESite sequences from the Genomic sequence.
- STRs (>50 bp)
- ABCC identified STR (2-16) sequences from the Genomic sequence.
- STRs (test)
- ABCC identified STR (2-16) sequences from the Genomic sequence.
- PuPys (>100 bp)
- ABCC Identified PuPy sequences (2-16bp)- stretches of pyrimidine/purine repeats. Identified by scanning genomic sequences.
- mSTRs (>50 bp)
- ABCC identified MonoSTR sequences from the Genomic sequence.
- mPuPys (>100 bp)
- ABCC Identified Mono PuPy sequences - stretches of pyrimidine/purine repeats. Identified by scanning genomic sequences.
- lSTRs (>50 bp)
- ABCC identified Long (17-100) STR sequences from the Genomic sequence.
- lPuPys (>100 bp)
- ABCC Identified Long (17-100) PuPy sequences - stretches of pyrimidine/purine repeats. Identified by scanning genomic sequences.
- SegDups (5k/2m/90; ABCC)
- ABCC Segmental Duplications (each "arm" > 5kbp; separation < 2mbp; <90% RepeatMasker content)
- LINEs (>2k bp)
- RepeatMasker Flagged LINE elements > 2kbp in length
- SINEs (>200 bp)
- RepeatMasker Flagged SINE elements > 200 bp in length
- LTRs (>300 bp)
- RepeatMasker Flagged LTR elements > 300 bp in length
- RMSK Elements (>50 bp, ABCC)
- Genomic RepeatMasker Elements > 50 bp in Length.
- Gene Based Macaque Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Dog Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Human Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Horse Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Mouse Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Cat Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Chimp Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Rat Synteny Block
- Precursor Syntenic Block Predictions
- Gene Based Opossum Synteny Block
- Precursor Syntenic Block Predictions
- Contigs
- Assembly Contigs and Alignments
- Assembly GAPs
- Genome Assembly Gaps. Parsed from Mapview Information.
- Plasmid Mate Pair Alignments
- ABCC Plasmid Mate Pair GMap Alignments
- Bac Mate Pair Alignments
- ABCC Bac Mate Pair GMap Alignments
- Fosmid Mate Pair Alignments
- Fosmid Mate Pair GMap Alignments
- Sequence Mate Pair Alignments
- ABCC Sequence Mate Pair GMap Alignments
- Trace Alignments
- ABCC GMapped Sequence Trace (Availability subject to performance issues, may only represent a subset of all traces.)
- tBubble Alignments
- Bubble Alignments from Traces
- Flap Alignments
- Flap Alignments
- STRs from traces
- ABCC trace STR Polymorphisms. Traces were aligned to the reference genome and STR Polymorphisms were identified - red means a predicted polymorphic STR.
- InDels from Traces
- ABCC identified Strain Indel Polymorphisms. Traces were aligned to the reference genome and InDel Polymorphisms were identified - red means a predicted insertion, blue means predicted deletion polymorphism.
- Diffs from Traces
- ABCC identified Strain Diff Polymorphisms. Traces were aligned to the reference genome and Complex Difference Polymorphisms were identified..
- SNPs from Traces
- ABCC GMapped SNP Sequences from Traces.
- Insertions from Traces
- ABCC identified Strain Intron Polymorphisms. Traces were aligned to the reference genome and InDel Polymorphisms were identified - red means a predicted insertion, blue means predicted deletion polymorphism.
- GMap SNP Alignments (ABCC)
- ABCC GMapped SNP Sequences - used to check GMap alignment capabilities
- EST Alignments
- ABCC GMapped EST Alignments of Mouse ESTs from Genbank.
- miRNA Alignments
- positional mapping of miRNA genes from miRBase using GMap
- Unigene Alignments
- ABCC GMapped Unigene Alignments.
- xUnigene Alignments
- ABCC GMapped Unigene Alignments from non-horse species.
- Refseq Alignments
- ABCC GMapped Refseq Alignments (Genes_mRNAs)
- xRefseq Alignments
- ABCC GMapped Refseq mRNAs
- Ensembl mRNAs Alignments
- ABCC GMapped Ensembl mRNA Alignments
- xEnsembl mRNAs Alignments
- ABCC GMapped Xeno Ensembl mRNA Alignments
- MGC Alignments
- ABCC GMapped MGC Alignments using MGC Sequences for Mouse
- MGC xAlignments
- ABCC GMapped MGC Alignments using MGC Sequences for nonHorse
- miRNA Promoters
- miRNA Promoter Regions (defined as -1500 --> +200 of transcription start site
- GMap Affy Consensus Probes
- ABCC GMapped Affymetrix Consensus sequences for Affy Chips
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Generic genome browser version 1.64