NIA Mouse Gene Index

All tables are tab-separated text files. Some fields contain comma-separated lists

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
Protein-coding
Gene symbol
Unigene clusters
TIGR clusters
DoTS clusters

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
Potentially wrong strand
Number of introns with correct splice concensus
Is gene
Protein-coding
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)

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
Unigene clusters
TIGR clusters
DoTS clusters

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=good splice sites, 0=bad splice sites, -9999=non intron gap, 2=clone-link gap)

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