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Polymorphic Retrotransposon Information
Database ID: RIP_Alu_chr1_024_01
Original ID: Yd6JX352|16745
Class: SINE
Family: Alu
Subfamily: Yd8
Associated disease: NA
Sequence of Alu insertion and 400bp flanking on each side (5' flanking-TSD1-REPEAT SEQUENCE-TSD2-3' flanking)
("nnnnn" --> unknown TSD; "NNNNNNNNNN" --> unknown Repeat Sequence): tcccagctactcgggaggctgaggcaggagaatggcgtgaacctgggaggcggagcttgcagtgagccgagatcgcgccactgcactccatgctgggtga
cggagcgaaactccgtctcaaaaaaaaaaaaaatcatatatatatgtattagaagtgcactgattaataaggaaagctgtttccaatatattgtcaaagt
ttacaaaactatatatacatggtaatctcaatcatacacataggttacccatacacatatccaagggaaagcaacacagcaaggtcttaacaactggtgt
gtctacatgatggcattgttagtttttgctgggagggggatgttcctaatttttgaggaatggtaaacacgcattgtttttatAAGAATATGAATATTAT
CCTGTAATCCCAGCACTTTGAGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAT
TAGCCGGGCGCAGTGGTGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGAAGGCGGAGCTTGCAGTGAGCGGAG
ATCGCGCCACAGCACTCCCGCCTGGGCGACAGAACGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAGAATATGAATATTATttataaagggagct
gctaggtgtggtggctctgcctgtaaccccagctagtcaggaggctgaggcaggaggatcacttgagccccagagtttgagaccagcttgggcaacatag
caagaccctgtctctggaaaaaaaaaaaagtttttaaaataaaggtagctaggccgggcgtggtggctcacacctgtaatctcagcactttgggaggctg
aggcgggcagatcacggggtcaggagtttgaacattgtgaaaccccatctctactgaaaatacaaaaaatcagctgggcatggtggcgggtgcctgtaat
cccagctacttgggaggctgaggcaggagaatcacttgaacccgggaggcggaggttgcagtgagctga
Forward Primer: ATCCAAGGGAAAGCAACACA
Reverse Primer: CACACCTAGCAGCTCCCTTTAT
Annealing Temperature: 60.0 °C .
PCR Product Size (Filled): 452 bp.
PCR Product Size (Empty): 166 bp.
Ascertaining Method: Candidate screening|Trace comparison
Genome Source: UCSC
Remarks: NA
Polymorphism Frequencies and Genotypes:
| Ethnic Group | Sample Size | Allele Frequency | +/+ | +/- | -/- | Unbiased Heterozygosity |
|---|
| European/German Caucasian | 20 | 1.000 | 20 | 0 | 0 | 0.000 | | Egyptian/South Americans | 20 | 1.000 | 20 | 0 | 0 | 0.000 | | African American | 20 | 0.725 | 11 | 7 | 2 | 0.409 | | Asian | 20 | 1.000 | 20 | 0 | 0 | 0.000 | | All Samples | 80 | 0.931 | 71 | 7 | 2 | 0.129 |
Position: chr1:24674119-24674388 (Back to Genome Browser)
Band: 1p36.11
Genomic Size: 268
Strand: +
View DNA for this feature
Reference(s): - Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA. Comprehensive analysis of two Alu Yd subfamilies. J Mol Evol. 2003;57 Suppl 1:S76-89.PMID: 15008405.
- Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural genetic variation caused by transposable elements in humans. Genetics. 2004 Oct;168(2):933-51. PMID: 15514065.
Description dbRIP currently contains all Alu, L1, and SVA insertion loci that are known to be polymorphic among human populations. The database deploys the utilities of UCSC genome broswer and allows querying and browsing of these loci alongside other existing genome annotations.
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