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Comparative analysis of conserved elements between duplicated genes provides a powerful approach …
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Biology Articles » Evolutionary Biology » Comparative Genomics » Comparative genomics using Fugu reveals insights into regulatory subfunctionalization » Tables
Tables - Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
Table 1
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Co-ortholog nomenclature and genomic locations in the Fugu genome
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Human gene*
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Co-ortholog name†
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Fugu scaffold (S) location (kb)‡
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Length (kb)§
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Prop 'N's (%)¶
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Fugu protein accession code¥
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BCL11A
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bcl11a.1
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S113: 140.8-518.9
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378.1
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2.98
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NEWSINFRUP00000142044
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bcl11a.2
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S62: 603.7-740.4
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136.7
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0.18
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NEWSINFRUP00000144873
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EBF1
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ebf1.1
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S97: 400.4-483.3
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82.9
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0.82
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NEWSINFRUP00000127762
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ebf1.2
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S71: 999.3-1,091.7
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92.4
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1.90
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NEWSINFRUP00000148373
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FIGN
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fign.1
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S36: 382.6-486.8
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104.2
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0.16
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NEWSINFRUP00000153680
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fign.2
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S46: 126.9-219.9
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93
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0.39
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NEWSINFRUP00000177971
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PAX2
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pax2.1
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S86: 541.7-669.8
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128.1
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0.29
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-
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pax2.2
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S59: 768.9-898.3
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132.7
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3.59
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-
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SOX1
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sox1.1
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S42: 1,020-1,105
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85
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1.49
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[Swiss-Prot: Q6WNU3_FUGRU]
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sox1.2
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S313: 107.2-174.9
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67.7
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8.9
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[Swiss-Prot: Q6WNU2_FUGRU]
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UNC4.1
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unc4.1.1
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S15: 761.1-825.5
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61
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0.32
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NEWSINFRUP00000154395
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unc4.1.2
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S40: 1,435-1,537
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102
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0.96
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NEWSINFRUG00000161008
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ZNF503
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znf503.1
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S86: 7-220
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213
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3.64
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NEWSINFRUP00000181530
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znf503.2
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S59, S29 (all)
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148.5
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3.22
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NEWSINFRUP00000181454
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| *Name of human gene ortholog. †Nomenclature of novel Fugu co-orthologs. ‡Location and extent of Fugu genomic scaffold used in multiple alignment. §Length of Fugu genomic region used in multiple alignment. ¶Proportion of Fugu genomic region that is made up of unfinished sequence (that is, runs of 'N's). ¥The protein accession code for each co-ortholog. These were derived either from Ensembl (v40.4b) or from SwissProt. Protein sequences for pax2.1 and pax2.2 were incomplete in both Ensembl and SwissProt and were reconstructed using alignments of full-length amino acid sequences from other species. |
Table 2
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Tajima relative rate tests of overlapping co-orthologous CNE in Fugu
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Gene region*
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No. of overlapping pairs†
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No. of CNE pairs with p > 0.05‡
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No. of CNE pairs with p ≤ 0.05§
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% of CNE pairs with p ¶
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Co-ortholog 1
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Co-ortholog 2
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BCL11A
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20
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15
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1
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4
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25
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EBF1
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7
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5
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1
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1
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21
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FIGN
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28
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21
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5
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2
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25
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PAX2
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43
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34
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4
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5
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21
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SOX1
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6
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5
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0
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1
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17
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UNC4.1
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20
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15
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0
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5
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25
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ZNF503
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84
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62
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5
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17
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26
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| *Gene region. †Total number of overlapping CNEs within gene region. ‡Numbers of overlapping CNE pairs with no significant difference in substitution rates (that is, p values of > 0.05). §The number of overlapping CNEs that exhibit a significant difference in substitution rate (that is, p value ≤ 0.05) in the CNE sequence in the vicinity of one co-ortholog over that in the other. ¶The percentage of overlapping CNEs with significantly different substitution rates in either co-ortholog as a proportion of the total number of overlapping CNEs. |
Table 3
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Co-ortholog CNEs that are also conserved in the vicinity of trans-dev paralogs in the human genome
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Gene region
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Co-ortholog 1
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Co-ortholog 2
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Gene paralog in the vicinity of the dCNE(s)
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BCL11A
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CRCNE00002445
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CRCNE00004614
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BCLL1B
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CRCNE00002557
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-
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CRCNE00002548
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CRCNE00004648
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CRCNE00002544
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CRCNE0004643
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CRCNE0004644
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CRCNE00002540
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-
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EBF1
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CRCNE00010771
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-
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EFB3
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-
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CRCNE00010818
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CRCNE00000027
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CRCNE00010823
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CRCNE00010778
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CRCNE00010827
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CRCNE00010787
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-
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EBF1
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CRCNE00010772
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CRCNE00010820
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EBF1/2/3/4
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PAX2
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CRCNE00000064
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CRCNE00000133
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PAX8
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PAX2
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CRCNE00000071
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CRCNE00000147
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PAX5
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CRCNE00000090
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CRCNE00000165
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CRCNE00000092
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CRCNE00000167
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CRCNE00000099
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CRCNE00000174
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SOX1
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-
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CRCNE00001926
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SOX2
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ZNF503
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CRCNE00010112
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CRCNE00004977
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ZNF703
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CRCNE00010147
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CRCNE00004994
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CRCNE00010126
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CRCNE00005024
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CRCNE00010167
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-
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CRCNE00010170
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-
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CRCNE00010187
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-
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CRCNE00010180
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-
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CRCNE00010176
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CRCNE00005013
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CRCNE00005015
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CRCNE00010165
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CRCNE00005011
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CRCNE00010161
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CRCNE00005008
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CRCNE00010046
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CRCNE00004906
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CRCNE00010156
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CRCNE00005003
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CRCNE00010120
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CRCNE00004986
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| CNEs in each co-ortholog are referred to by their CONDOR database identifiers [53]. Each CNE was considered duplicated if the human sequence they are conserved to shows significant hit to a sequence elsewhere in the genome through BLAST. Any gene in the vicinity ( |
rating: 8.00 from 5 votes | updated on: 20 Jul 2007 | views: 5780 |
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