Table 5.
Largest Blocks of Segmental Duplication in the Rat Genome
|
Chromosome |
v.3.1begin |
v.3.1end |
Block size |
Homology |
Content |
|---|---|---|---|---|---|
| chr15 | 28153750 | 31785691 | 3631941 | chr15 | T-cell receptor |
| chr1 | 49778386 | 53005805 | 3227419 | chr1 | noRefseq, noRatmRNA, noRatEst, but homology to non-rat mRNA |
| chr1 | 30806167 | 33768308 | 2962141 | chr1, 3, 7, 12, 16 | noRefseq, noRatmRNA, limited RatEst |
| chr7 | 4210045 | 6569239 | 2359194 | chr7 | noRefseq, noRatmRNA, noRatEst, but homology to non-rat mRNA |
| chr1 | 5500 | 2196674 | 2191174 | chr1, 7, 9, 14 | noRefseq, noRatmRNA, limitedRatEst, subtelomeric homology |
| chr14 | 48526685 | 50326618 | 1799933 | chr14, 9 | noRefseq, noRatmRNA, RatEST |
| chr15 | 19229668 | 20983782 | 1754114 | chr15, 3, 12 | prostaglandin D2 receptor |
| chr15 | 4606290 | 6304612 | 1698322 | chr15 | MIC2 like 1/Rhombex40 |
| chr7 | 2608728 | 4103847 | 1495119 | chr7 | noRefseq, noRatmRNA, noRatEst, but homology to human mRNA |
| chr19 | 23253330 | 24673455 | 1420125 | chr14, 19 | noRefseq, noRatmRNA, noRatEst, but homology to non-rat mRNA |
| chr12 | 18092439 | 19509542 | 1417103 | chr12 | noRefseq, noRatmRNA, limited RatEst |
| chr6 | 138660326 | 140060338 | 1400012 | chr6 | Immunglobulin heavy chain variable region (IGHV) |
| chr17 | 67155883 | 68547346 | 1391463 | chr17 | noRefseq, noRatmRNA, RatEst |
| chr2 | 14691 | 1387166 | 1372475 | chr1, 2, 3, 7, 16 | noRefseq, limited RatmRNA and RatEST, subtelomeric |
| chr7 | 18156845 | 19521121 | 1364276 | chr7(prim), 8, 9 | noRefseq, noRatmRNA, RatEST |
| chr7 | 16446057 | 17651248 | 1205191 | chr7 | noRefseq, noRatmRNA, RatEST (conserved) |
| chr3 | 20974 | 1139288 | 1118314 | chr1, 2, 3, 7, 12, 15, 16 | noRefseq, noRatmRNA, RatEST |
| chr17 | 7851444 | 8937241 | 1085797 | chr17 | Cathepsin Ma |
| chr8 | 36551927 | 37612862 | 1060935 | chr8 | Atpase inhibitor |
| chr1 | 112988982 | 114038449 | 1049467 | chr1 | noRefseq, noRatmRNA, RatEST |
| chr5 | 78092980 | 79128821 | 1035841 | chr5 | alpha 2μ globulin PGCL3b Zfp37 |
| chr9
|
4870998
|
5902959
|
1031961
|
chr9, 14, 16
|
noRefseq, noRatmrna, RatEST
|
-
Blocks were defined as clusters of segmental duplication with <100 kb of intervening sequence between duplicons. The largest 22 blocks which were assigned to a chromosome are shown. For a complete listing of all blocks, see http://ratparalogy.gene.cwru.edu. Begin and end coordinates within build 3.1, block size, and homologous regions are shown. Content was based on assigned Refseq, Rat mRNA, and ESTs within intron/exon structure within the UCSC browser. aBest sequence match of Cathepsin M is on chromosome 5. bEstimated 20 copies, but only five copies can be distinguished within the assembly.
