SOAR: System for Orthologous Assignment by Reversals

• Experimental data
  
  Human X chromosome [992 genes]
  Mouse X chromosome [1030 genes]
  Rat X chromosome [899 genes]
  
  
• Original gene data from GenBank
  
  Human X chromosome [download]
  Mouse X chromosome [download]
  Rat X chromosome [download]
  
  
• Breakpoint graphs showing genome rearrangements by reversals
  
  
  Human vs. mouse X chromosomes 
  
  
  Human vs. rat X chromosomes
  
  
  Mouse vs. rat X chromosomes 
  
  
• Dot-plot graphs showing pair-wise ortholog mapping
  
  Human vs. mouse X chromosomes [eps file]
  Human vs. rat X chromosomes [eps file]
  Mouse vs. rat X chromosomes [eps file]
  
  
• Orthologous pairs obtained from INPARANOID and SOAR
  
  

  	INPARANOID	SOAR
  Human vs. mouse X chromosomes	527 pairs	583 pairs
  Human vs. rat X chromosomes	468 pairs	518 pairs
  Mouse vs. rat X chromosomes	542 pairs	599 pairs

• Regarding synteny block 279
  
  Synteny block 279 was constructed by comparing:
      human NCBI build 30, June 2002; UCSC hg12
      mouse MGSC v3, Feb 2002; UCSC mm2
  
  But, we used the following assemblies for experiments:
      human NCBI build 34, July 2003; UCSC hg16
      mouse NCBI build 32, Oct 2003; UCSC mm4
      rat Baylor HGSC v. 3.1, Jun 2003; UCSC rn3
  
  A tool at http://genome.ucsc.edu/cgi-bin/hgLiftOver can convert genome coordinates between assemblies. We obtain the following block correspondence:
      human NCBI build 32: chrX:78691856-83712889
       human NCBI build 34: chrX:82083913-87212145
  
  A total of 13 annotated gene were found in the block chrX:82083913-87212145
      1. gene490_82090841_82214772_true_RPS6KA6(NM_014496)_
          mouse ortholog from SOAR:       gene415_63258690_63262523_true_Pnck(NM_012040)_
          Blast homolog hits in mouse:        gene964_147279119_147386484_false_Rps6ka3(NM_148945)_ 1128 0.0
                                                            gene483_67544602_67578525_true_Prkx(NM_016979)_ 206 2e-054
                                                            gene415_63258690_63262523_true_Pnck(NM_012040)_ 182 2e-047
                                                            gene109_12069236_12394745_true_Cask(NM_009806)_ 166 2e-042
                                                            gene978_149507713_149509336_true_LOC237188(XM_205338)_ 127 1e-030
                                                            gene867_131931446_132057526_false_Pak3(NM_008778)_ 114 7e-027
                                                            gene275_42143110_42193522_false_Mst4-pending(NM_133729)_ 103 1e-023
  
      2. gene491_82348182_82529318_true_FLJ30678(NM_144657)_
          mouse ortholog from SOAR:       gene704_101348568_101470433_true_D030011N01(XM_142098)_
          Blast homolog hits in mouse:        gene704_101348568_101470433_true_D030011N01(XM_142098)_ 1051 0.0
  
      3. gene492_82961014_82961753_false_MGC42638(NM_178567)_
          mouse ortholog from SOAR:       gene722_104749596_104753541_false_LOC237005(XM_136032)_
          Blast homolog hits in mouse:        gene451_64096306_64097693_true_LOC236864(XM_135925)_ 102 1e-024
                                                            gene720_104670739_104671667_false_4930524E20Rik(XM_284734)_ 96 1e-022
                                                            gene719_104668169_104669098_false_LOC237009(XM_142081)_ 96 1e-022
  
      4. gene493_83073309_83114807_false_LOC139322(NM_198450)_
          mouse ortholog from SOAR:       gene708_102084774_102145795_false_9430083G14Rik(NM_026565)_ *
          Blast homolog hits in mouse:        gene708_102084774_102145795_false_9430083G14Rik(NM_026565)_ 374 e-105
                                                            gene561_84106040_84155973_false_0610008C08Rik(NM_026673)_ 115 9e-028
  
      5. gene494_83119157_83145277_true_LOC340562(XM_291339)_ 
          mouse ortholog from SOAR:       gene709_102157671_102180122_true_4930404K22Rik(XM_136025)_
          Blast homolog hits in mouse:        gene709_102157671_102180122_true_4930404K22Rik(XM_136025)_ 283 1e-077
                                                            gene948_143210648_143213855_true_Sat1(NM_009121)_ 115 3e-027
  
      6. gene495_83270948_83298784_false_ZNF6(NM_021998)_ 
          mouse ortholog from SOAR:       gene711_102373892_102399439_false_A230078I01(NM_177747)_
          Blast homolog hits in mouse:        gene557_83813518_83818761_true_Zfx(NM_011768)_ 890 0.0
                                                            gene711_102373892_102399439_false_A230078I01(NM_177747)_ 500 e-143
                                                            gene150_19632369_19642448_true_D930016N04(NM_183185)_ 179 3e-046
                                                            gene148_19583118_19615241_true_6330583I20Rik(XM_205300)_ 173 2e-044
                                                            gene407_62945330_62961659_false_Zfp275(NM_031494)_ 157 1e-039
                                                            gene308_45990656_46008771_false_9530049C15Rik(NM_030139)_ 131 7e-032
                                                            gene409_63013791_63026848_false_Zfp92(NM_009566)_ 125 5e-030
  
      7. gene496_83304259_83406605_true_POF1B(NM_024921)_ : Pof1b-pending 
          mouse ortholog from SOAR:       gene712_102411793_102472017_true_Pof1b-pending(NM_181579)_
          Blast homolog hits in mouse:        gene712_102411793_102472017_true_Pof1b-pending(NM_181579)_ 949 0.0
  
      8. gene497_83888043_84074166_true_FLJ38564(NM_152579)_
          mouse ortholog from SOAR:       (null)
          Blast homolog hits in mouse:        ***** No hits found ******
  
      9. gene498_83891369_84074423_true_CHM(NM_000390)_ 
          mouse ortholog from SOAR:       gene713_102814812_102958881_true_Chm(NM_018818)_ *
          Blast homolog hits in mouse:        gene713_102814812_102958881_true_Chm(NM_018818)_ 1028 0.0
                                                            gene442_63907951_63914554_false_Gdi1(NM_010273)_ 112 3e-026
  
      10. gene499_84104403_84113201_true_LOC347428(XM_293345)_ 
          mouse ortholog from SOAR:       (null)
          Blast homolog hits in mouse:        ***** No hits found ******
          
      11. gene500_84175482_84859447_false_DACH2(NM_053281)_
          mouse ortholog from SOAR:       gene714_103071623_103609259_false_Dach2(NM_033605)_ *
          Blast homolog hits in mouse:        gene714_103071623_103609259_false_Dach2(NM_033605)_ 801 0.0
          
      12. gene501_85544674_85696907_false_KLHL4(NM_019117)_
          mouse ortholog from SOAR:       gene717_104247886_104334064_false_C130018J01Rik(NM_172781)_
          Blast homolog hits in mouse:        gene717_104247886_104334064_false_C130018J01Rik(NM_172781)_ 1032 0.0
                                                            gene158_21878090_22023872_true_Bklhd2(NM_026167)_ 256 1e-069
          
      13. gene502_86774112_86781636_false_CPXCR1(NM_033048)_ 
          mouse ortholog from SOAR:       gene725_106231102_106260520_false_LOC382239(XM_356353)_
          Blast homolog hits in mouse:        gene725_106231102_106260520_false_LOC382239(XM_356353)_ 188 1e-049
  
  In the above, there mouse genes labeled with '*' can be found within the block of mouse MGSC v3 chrX:100,126,658-105,951,929. Please see http://genome-mm2.cse.ucsc.edu/cgi-bin/hgGateway .
  

Xin Chen, 11/02/2004