Table 1 Details provided in STaRRRT
From: STaRRRT: a table of short tandem repeats in regulatory regions of the human genome
Column name | Description of field | Example of entry |
|---|---|---|
Chrom | Chromosome number on which STR is located | chr1 |
chromStart | Start position on chromosome of the gene | 28218048 |
chromEnd | End position on chromosome of the gene | 28241236 |
cdsStart | Coding sequence start | 28218673 |
cdsEnd | Coding sequence end | 28240954 |
Strand | Strand on which the gene occurs | _ (negative) |
knownGeneId | KnownGene database identifier | uc001bpe.1 |
refSeqId1 | RefSeq database identifier | NM_002946 |
ensGeneId | Ensembl database identifier | ENST00000373912 |
sourceAcc | GenBank transcript accession number | NM_002946.3 |
hgncSymbol2 | HGNC gene symbol | RPA2 |
U133Id | Affymetrix GeneChip array identifier | U133A:201756_at; |
U133Plus2Id | Affymetrix GeneChip Plus2.0 array identifier | 201756_at |
Category | Type of gene (coding or noncoding) | coding |
txPos3 | Position in relation to the TSS | −1910 |
srStart4 | Start position on chromosome for the STR | 28243107 |
srEnd | End position on chromosome for the STR | 28243146 |
Period5 | Length of the repeat unit in the STR | 2 |
numRepeats | Number of copies of the repeat unit | 19.5 |
srLength | Total length of the STR | 39 |
consensusSize | Number of bases in the consensus sequence | 2 |
perMatch6 | % match of STR to consensus sequence; purity | 100 |
perIndel | Percent insertions and/or deletions in the STR | 0 |
Score | Alignment score (minimum = 50) | 78 |
A | Percent of A's (adenine) in the repeat unit | 0 |
C | Percent of C's (cytosine) in the repeat unit | 0 |
G | Percent of G's (guanine) in the repeat unit | 48 |
T | Percent of T's (thymine) in the repeat unit | 51 |
Entropy | Entropy | 1 |
Sequence | Consensus sequence of the repeat unit; motif | TG |