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. 2006 Sep;174(1):349–362. doi: 10.1534/genetics.105.054346

TABLE 1.

X chromosome near-telomeric and nontelomeric loci

Locus Full name Codons Map Seq. map Rec. MCU No. int Int bp
Near telomeric
    CG2995 486 1A1 0.11 0.23 0.45 5 278
    cin cinnamon 449 1A1 0.11 0.23 0.45 3 224
    y yellow 441 1A5 0.22 0.33 0.38
    sc scute 332 1A8 0.25 0.37 0.49
    l(1)sc lethal of scute 255 1B1 0.27 0.38 0.61
    ase asense 323 1B3 0.32 0.43 0.47
    l(1)1Bb Exportin 6 613 1B4 0.33 0.44 0.64 5 438
    EG:171D11.2 467 1B5 0.35 0.46 0.51 4 295
    l(1)1Bi lethal l(1)1Bi 578 1B12 0.49 0.60 0.57 3 165
    su(wa) Suppressor of white-apricot 515 1E1 0.90 0.96 0.55 5 257
    CG11403 577 1E4–5 1.09 1.13 0.56 2 108
    futsch futsch 456 2A3 1.29 1.29 0.65 5 367
    sta stubarista 270 2B1 1.34 1.33 0.82 1 187
    dor deep orange 557 2B5 1.52 1.47 0.67 2 103
    Sum 6319 35 2422
Nontelomeric
    per period 618 3B2–3 2.55 2.22 0.74 3 157
    Mcm3 Minichromosome maintenance 3 496 4F5 5.17 3.59 0.65 2 72
    ND75 NADH:ubiquinone reductase 75-kDa subunit precursor 547 7E1 8.10 4.26 0.71 3 149
    RpII215 RNA polymerase II 215kD subunit 743 10C6–7 11.41 4.19 0.58 1 104
    Cyp28c1 429 10F1 11.67 4.16 0.65 4 109
    g garnet 528 12B4–6 13.56 3.80 0.63 4 152
    Fur2 Furin 2 540 14C1 16.21 3.07 0.61 6 278
    Zw Zwischenferment 517 18D13 19.50 1.92 0.82 2 140
    run runt 488 19E2 20.51 1.54 0.72 1 187
    Sum 4906 26 1348

Gene symbols and cytogenetic map (map) and sequence map (Seq. map) positions in Drosophila melanogaster are from FlyBase (Drysdale et al. 2005) and Map Viewer of the National Center for Biotechnology Information (NCBI) website (http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7227&chr=X). Seq. map positions (megabases) are measured from the distal end of the chromosome (Wheeler et al. 2005). Codons are the number of aligned codons. Rec. represents recombination rates (centimorgans per megabase) estimated by fitting a polynomial regression of genetic map on physical map locations; the estimates are labeled “Rp” in Hey and Kliman (2002). Major codon usage (MCU) is the proportion of major codons in a gene. Codon preferences are from Akashi (1995). MCU values are the averages for the six extant D. melanogaster subgroup species. Note that map and Seq. map positions do not point to identical locations on the X chromosome ideograms in Figures 2 and 3. No. int and Int bp represent numbers of introns and numbers of aligned intronic nucleotides, respectively, for each locus.