NIA Mouse Gene Index 3.0

Field Annotations in Output Tables

• U-cluster name
• Annotation
• Symbols, comma separated

• U-cluster name
• Chromosome
• Strand
• Start position (starts from 0)
• End position
• Members, comma separated
• Intronic
• Sum of all exons lengths
• Gene member sources, binary coded (NIA=1,Riken=2,Ensembl=4,RefseqXM=8,RefseqNM=16,GenBank=32,dbEST=64)
• Number of exons
• ORF length, aa
• Primary gene=1, pseudogene/copy=2
• Percent repeats
• Potentially wrong strand
• Number of introns with correct splice concensus
• Is gene (or gene candidate)
• Protein-coding gene
• Gene symbol

• Gene name
• Chromosome
• Strand
• Start position (starts from 0)
• End position
• Intronic
• Sum of all exons lengths
• Gene member sources, binary coded (NIA=1,Riken=2,Ensembl=4,RefseqXM=8,RefseqNM=16,GenBank=32,dbEST=64)
• Number of exons
• ORF length, aa
• Primary gene=1, pseudogene/copy=2
• Percent repeats
• Number of introns with correct splice concensus
• Protein-coding gene
• Gene symbol

• U-cluster name
• Chromosome
• Strand
• Number of exons
• Exon Sizes (comma separated)
• Exon start positions (comma separated)
• Number of exon forms
• Sizes of exon forms (comma separated)
• Start positions of exon forms (comma separated)
• Exon number for exach exon form (comma separated)
• Number of all possible introns (connections of exon forms)
• Intron starts (comma separated)
• Intron ends (comma separated)
• Intron status (comma separated) proper splice sites=4; bad splice sites=2; retained intron=1.
• ORF segment lengths, split into exons (comma separated)
• ORF segment starts in the genome (comma separated)

• U-cluster name
• Major transcript (mostly with. longest ORF)
• U-cluster score
• Transcript score

• U-cluster name with potentially wrong strand
• Better supported U-cluster with which the previous U-cluster overlaps

• Transcript name
• Annotation
• Symbols, comma separated
• Source of annotation

• Transcript name
• Chromosome
• Strand
• Start position (starts from 0)
• End position
• Members, comma separated
• Intronic
• Lengths
• Gene member sources, binary coded (NIA=1,Riken=2,Ensembl=4,RefseqXM=8,RefseqNM=16,GenBank=32,dbEST=64)
• Number of exons
• ORF length, aa
• Primary gene=1, pseudogene/copy=2
• Percent repeats
• Potentially wrong strand
• Number of introns with correct splice concensus

• n_match
• n_mismatch
• repeat_match
• N-count
• QgapCount
• QgapBases
• TgapCount
• TgapBases
• strand
• Qname
• Qsize
• Qstart (start from 0)
• Qend
• Tname
• Tsize
• Tstart (start from 0)
• Tend
• blockCount
• blockSizes
• qStarts (start from 0)
• tStarts (start from 0)
• Intron status (1=splice sites, 0=no splice sites, -9999=non intron gap, 2=clone-link gap)

• n_match
• n_mismatch
• repeat_match
• N-count
• QgapCount
• QgapBases
• TgapCount
• TgapBases
• strand
• Qname
• Qsize
• Qstart (start from 0)
• Qend
• Tname
• Tsize
• Tstart (start from 0)
• Tend
• blockCount
• blockSizes
• qStarts (start from 0)
• tStarts (start from 0)

• Transcropt name
• ORF start, bp (start from 0)
• ORF end, bp
• ORF break point, bp (if ORF consist of 2 overlapping parts, then this is the end of 2 parts)
• ORF length, aa
• First aminoacid
• Kozak consensus: 0=weak or undetermined, 1=adequate, 2=strong, 3=optimal

• Transcript name
• Transcript length
• Total repeat length
• Repeat block lengths (comma separated)
• Repeat block starts (start from 0, comma separated)

• Alignment names (sequence name: copy number)

• n_match
• n_mismatch
• repeat_match
• N-count
• QgapCount
• QgapBases
• TgapCount
• TgapBases
• strand
• Qname
• Qsize
• Qstart (start from 0)
• Qend
• Tname
• Tsize
• Tstart (start from 0)
• Tend
• blockCount
• blockSizes
• qStarts (start from 0)
• tStarts (start from 0)
• First block included (start from 0)
• Last block included