Hagfish HOX sequences

Downloads:

  • Raw data in fasta format
  • Alignment of raw data with annotation
    See here only if you really want to know which sequences are not Hox and why.
  • Index of PCR Sequences
  • Unique Hox genes
  • All Hagfish Hox nucleic acid sequences in in fasta format as shown in the table below.
  • Alignment of the nucleic acid sequences trimmed to the blocks that are present in most original sequences.
  • All Hagfish Hox amino acid sequences in aligned form
  • A simple UPGMA tree of the amino acid sequences was used to check the assignment of the sequences to their paralog groups.
  • Bootstrap support for paralog groups determined with neighbor joining and maximum parsimony
  • Summary of Hox sequences

    Total number of Hox sequences from PCR: 142
    Color key:
    Sequence found 3 or more times
    Sequence found twice
    Sequence found only
      Allelic variant of previous sequence

     

    Group Name # Protein Sequence Nucleic Acid Sequence Seq IDs
    1 Hox1_Z 3 HFNKYLTRARRLEIAAGLQLNEAQVKI------ CACTTTAACAAGTACTTGACGCGTGCCCGGCGGCTCGAGATCGCCGCTGGCCTGCAGCTGAACGAGGCACAGGTCAAGATC H1 = H1.sp6 H67.T7 H53.T7rc
    Hox1_Y 7 HFNKYLTRARRVEIAASLQLNETQVKI------ CACTTCAACAAGTACCTGACCCGTGCACGCAGGGTAGAGATCGCCGCTTCGCTGCAGCTCAACGAGACTCAGGTGAAGATC H3 = H3.T7 H45.T7 H63.T7 H76.T7 H12.T7rc H60.T7rc
    Hox1_X 14 HFNKYLTRRRRVEIATALQLNETQVKI------ CACTTCAACAAGTACCTAACGAGGCGTCGCCGTGTCGAGATCGCCACCGCCTTGCAACTCAATGAGACCCAGGTCAAGATA H6 H31 = H6.T7 H62.T7 H79.T7 H31.T7rc H35.T7rc
    2 Hox2_Z 10 EFHFNKYLCRPRRVEIAALLQLTERQVKVWFRK-- GAATTCCATTTTAACAAGTATCTATGTCGGCCTCGGCGGGTTGAAATTGCTGCGTTGCTGCAGCTCACTGAGCGACAGGTTAAAGTTTGGTTCCGAAAAT H57.T7rc H74.T7rc H69.T7rc
      Hox2_Z1 (1) KEFHFNKYLCRPRRVETAALLQLTERQVKVWFQ--- AAAAGGAGTTCCATTTTAACAAGTATCTATGTCGGCCTCGGCGGGTTGAAACCGCTGCGTTGCTGCAGCTCACTGAGCGACAGGTTAAAGTTTGGTTCCAAAA-- H71.T7
    3 Hox3_Z 3 HFNRYLCRPRRVEMANLLNLTERQIKIW----- TTCATTTCAACCGTTACTTGTGCCGCCCACGTCGTGTGGAGATGGCAAACCTCCTAAACCTTACTGAACGTCAGATCAAGATCTGGT H43.T7rc H44.T7rc
    Hox3_Y 1 HFNRYLCRPRRIEMANLLNLSERQIKI------ TCCACTTCAATCGCTACTTGTGTCGGCCACGCCGCATTGAGATGGCGAACCTTCTGAACCTCAGCGAGCGCCAGATAAAGATCTG H103EF.T7rc
    4-7 HoxM_Z1 12 DPRELEKEFHFNRYLTRRRRIEIAHTLCLSERQIKIWFQN-- GGATCCTCGAGAATTGGAGAAGGAGTTCCACTTCAACCGCTACCTGACTCGTCGTCGGCGCATCGAGATCGCCCACACCCTTTGCCTGAGTGAACGCCAAATCAAAATCTGGTTCCAAAAT H27r = H27.T7 H33.T7 [H41.T7] H42.T7rc H29.T7rc H73.T7rc
      HoxM_X (3) HFNRYLTRRRRIEIARALCLSERQIKI------ ----------------------------CACTTCAACCGCTACCTGACTCGTCGACGGCGCATCGAGATCGCCCGCGCCCTTTGCCTGAGTGAACGCCAAATCAAAATC------------
    HoxM_Z2 6 HFNRYLTRRRRIEIAHTLCLSERQIKIW----- CCACTTCAACCGCTACCTGACTCGGCGGCGGCGCATCGAGATCGCCCACACCCTGTGCCTTAGTGAACGTCAGATCAAGATCTGGTT H8 = H25.T7 H46.T7 H58.T7 [H25r] H8.T7rc
    HoxM_Z3 2 HFNRYLTRRRRIEIAHTLCLSERQIKI------ CACTTCAACCGTTATCTAACTCGTCGGCGACGCATCGAGATCGCCCACACCCTGTGCCTGAGTGAACGCCAGATCAAGATC H64.T7 H52.T7rc
    HoxM_Z4 9 HFNRYLTRRRRIEIAHTLCLSERQIKI------ CACTTCAATCGGTATCTGACCCGACGGAGACGCATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATC---- H9 = H32.T7 H47.T7 H51.T7 H9.T7.rc.trunc H50.T7rc
      HoxM_U1 (1) HFNRYLTRRRRIEIAHTLCLSERQIKIW----- TTCACTTCAATCGGTATCTGACCCGTCGGAGACGGATTGAGATAGCCCATACCCTTTGCCTCTCTGAGCGGCAGATCAAGATCTGGT H9.T7rc
    HoxM_W 4 HFNRYLTRRRrIEIAHALCLTERQIKI------ CATTTCAACCGCTACCTGACCCGGCGGCGGCCCATTGAGATCGCGCATGCCCTCTGTCTCACCGAGAGGCAGATCAAGATC H7rr = H7.T7 H37.SP6
     HoxM_Y 2 HFNRYLTRRRRIEIAHSLCLSERQIKI------ CACTTCAACCGCTACCTGACACGCCGGCGTCGCATTGAGATCGCACATTCCCTCTGCCTCTCTGAGCGCCAGATCAAGATC H28 = H28.T7
     HoxM_U2 2 HFNRYLTRRRRIEIRHALCLSERQIKI------ CCATTTCAACCGCTACCTGACGCGGCGGCGGCGCATTGAGATCCGGCACGCGCTTTGCCTCTCGGAGCGCCAGATCAAGATCTG H142EF.T7rc
    HoxM_V 9 DPAELEKEFHFNRYLSRRRRIEVAHALRLTERQIKIWFQNRR GATCCTGCAGAGTTGGAGAAGGAGTTCCATTTCAATCGGTACTTGAGCAGAAGGCGACGGATCGAGGTGGCACACGCGCTTCGTCTCACGGAGAGACAAATCAAAATCTGGTTCCAAAACCGCCGCAT H15r = H10.T7 H39 H77.T7 H11.T7 H85.T7rc H22.T7rc H39.T7rc
    8 Hox8_Z 11 LFNPYLTRKRRVEVSHSLGLSERQVKI------ CTTTTTAATCCCTACCTAACCCGCAAGCGACGTGTCGAGGTGTCTCATTCTCTGGGCCTCAGCGAGCGCCAGGTCAAGATC H16 = H16.T7 H23.T7 H30.T7 H34.T7 H34.SP6rc H72.T7rc H65.T7rc H70.T7rc
    Hox8_Y 3 LFNPYLTRKRRIEVSHALGLTERQVKI------ CTCTTCAATCCATACCTGACACGCAAGAGACGCATCGAGGTGTCACACGCGTTGGGCCTCACAGAACGCCAGGTGAAAATC H129EF.T7
    Hox8_X 2 LFNPYLTRKRRIEVSHALGLTERQVKI------ CTGTTCAACCCGTACCTGACGCGGAAGAGGCGCATCGAGGTGTCGCACGCGCTCGGCCTCACGGAACGCCAGGTGAAGATC H147EF.T7
    Hox8_W 3 LFNPYLTRKRRMEVSHALGLSERQVKI------ CTCTTCAACCCGTACTTGACTCGAAAACGCCGCATGGAGGTATCACACGCCCTGGGCTTGAGCGAGCGGCAGGTGAAAATC H121EF.T7
    9 Hox9_Z1 20 YQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKI------ GTACCAGACCCTTGAGCTGGAAAAGGAGTTCCTTTTTAACATGTACCTGACACGCGATCGCCGCTATGAGGTTGCGCGGGTCTTGAACCTCACAGAGAGACAAGTGAAGATT H20 = H18.T7 H26.5E5T7 H15.5E52.SP6 H5.5E5T7 H28.5E52.T7 H215E5.T7rc H22.5E5.T7rc H7.5E5T7rc H88.T7rc H68.T7rc H40.SP6rc H56.T7rc H20.SP6rc H59.T7rc
      Hox9_Z2 (1) LFNMYLTRDRRYEVERVLNLTERQVKI------ CTTTTTAACATGTACCTGACACGCGATCGCCGCTATGAGGTTGAGAGGGTCTTGAACCTCACAGAGAGACAAGTGAAGATT H18 (typo?)
    Hox9_V 1 ----------LFNMYLTRDRRYEVARVLNLTERQVKI------ -------------------------------CTGTTCAACATGTACCTGACGCGGGATCGACGCTATGAGGTGGCTCGGGTACTGAACCTGACTGAGAGGCAAGTGAAGATC H83.T7
    Hox9_Z3 5 ----------LFNMYLTRDRRYEVERVLNLTERQVKI------ ----------------------------TCCTCTTCAACATGTACCTAACGCGGGACCGTCGCTACGAGGTCGCTCGGGTGCTGAATCTCACGGAGCGACAAGTGAAAATCT H55.T7rc
    Hox9_Z4 1 HQILELDKEFLFNTYLTRDRRYEVARLLNLTERQVKI------ CACCAGATCCTGGAGCTGGATAAGGAGTTCCTCTTTAACACCTACCTGACCCGGGACCGCAGGTACGAGGTGGCTCGGCTGCTGAACCTCACCGAGAGACAGGTCAAAATCTG H22.5E52.SP6rc
    Hox9_Y 4 HQTLELEKEFLFTKYLTRDRRYEVARVLDLSERQVKI------ GCACCAAACGCTCGAGCTCGAGAAGGAGTTTTTGTTTACCAAGTACTTGACGCGGGACCGTCGGTACGAGGTCGCACGAGTACTGGATCTTAGCGAAAGGCAGGTCAAGATA H31.5E52.T7 H33.5E52.SP6
      Hox9_Z5 (1) LFTKYLTRDRRYEVARVLDLSERQVKI------ TTTGTTTACCAAGTACTTGACGCGGGACCGTCGGTACGAGGTCGCACGAGTACTGGATCTTAGCGAAAGGCAGGTCAAGATA H19.T7rc
    Hox9_X 3 YQTLELEKEFLFNMYLTRDRRHEVARALNLTERQVKI------ ATATCAGACCCTAGAGCTTGAAAAGGAATTTTTATTCAACATGTATCTCACGAGGGACCGAAGGCATGAGGTGGCACGCGCACTGAACCTGACAGAGAGGCAGGTTAAGATT H30.5E52.T7 H12.5E52.SP6rc
    Hox9_W 7 YQTLELEKEFLYDMYLTRDRRYEVARILSLTERQVKI------ ATATCAGACTCTAGAGCTGGAGAAGGAGTTTCTCTACGACATGTATCTGACAAGGGACCGGCGCTACGAGGTGGCCCGCATCCTCAGCTTAACGGAGAGACAAGTGAAGATC H18.5E52.T7 H235E5.T7 H5.5E52.SP6rc H11.5E52.SP6rc H87.T7rc H75.T7rc
    10 Hox10_Z 21 QQTLELEKEFLFNMYLTRERRVEISRYVNLTDRQVKI------ GCAGCAGACCCTCGAGCTGGAGAAGGAGTTCCTTTTCAACATGTACCTGACGAGGGAGCGCCGGGTGGAGATTAGTCGCTACGTTAACCTTACTGACCGGCAAGTCAAGATC H2.sp6 H2.all H78.T7 H5.T7 H21.T7 H49.T7 H17.5E5T7 H84.T7rc H205E5.T7rc H54.T7rc H66.T7rc H82.T7rc H24.T7rc
    Hox10_Y1 7 YQTLELEKEFLFNTYLTRERRLEISRSVHLTERQVKI------ ATATCAGACTCTCGAATTAGAGAAAGAGTTCCTCTTTAACATGTACCTGACGCGGGAGCGCCGCCTGGAGATCAGCCACAGTGTGAACTTGACCGATCGACAAGTTAAGATC H10.5E5T7 H12.5E5T7 H15.5E5T7 H14.5E52.SP6 H26.5E52.T7 H3.5E5T7rc
      Hox10_Y2 (1) SQTLELEKEFLFNMYLTRAGRLEISHSVNLTDRQVKI------ ATCTCAGACTCTCGAATTAGAGAAAGAGTTCCTCTTTAACATGTACCTGACGCGCGCGGGCCGCCTGGAGATCAGCCACAGTGTGAACTTGACCGATCGACAAGTTAAGATC H27.5E5T7
    Hox10_X 2 HQTLELEKEFLFNMYLTRERRLEISRSVHLTDRQVKI------ GCACCAGACTCTGGAGCTGGAGAAGGAGTTCCTCTTCAACATGTACTTGACTCGGGAGCGTCGCCTGGAGATCAGCCGCAGCGTGCACCTCACCGACAGGCAAGTCAAAATC H9.5E5T7 H6.5E52.SP6
    Hox10_W 1 HQTLELEKEFLFNMYLTRERRLEISKSVHLTDRQVKI------ GCACCAGACGCTGGAGCTGGAGAAGGAGTTCCTCTTCAACATGTACCTGACCCGTGAGCGCCGCCTAGAGATCAGCAAGAGCGTCCACCTGACGGACAGACAGGTCAAGATC H10.5E52SP6
    Hox10_W2 5 RQTLELEKEFLFNMYLSRERRLEISRSINLTDRQVKIW----- GCGCCAGACGCTGGAGCTGGAGAAGGAGTTCTTGTTCAACATGTATCTGTCTCGGGAGCGCCGCCTGGAGATCAGCCGCAGTATCAACCTGACCGACAGACAGGTCAAGATCTGG H16.5E52.SP6
    11 Hox11_Z 11 FQTRELEREFFFNVYINKEKRQQLSCLLDLTDRQVKI------ GTTCCAAACACGAGAACTGGAGCGTGAGTTTTTCTTCAATGTTTACATCAACAAGGAAAAGCGGCAACAGCTCTCATGCCTGCTGGACCTCACTGACCGACAAGTGAAAATC H11.5E5T7 H32.5E5T7 H30.5E5T7 H31.5E5T7 H6.5E5T7rc H25.5E5T7rc H29.5E5T7rc H27.5E52.T7rc H1.5E52.SP6rc [H19.5E52.T7rc]
    Hox11_Y 2 YQIRELEREFFFNVYINKEKRVQLSRMLNLTDRQVKI------ GTACCAGATCCGTGAGTTGGAACGCGAGTTCTTTTTCAACGTTTACATCAACAAAGAAAAGCGAGTGCAGCTTTCGAGGATGTTGAATCTGACGGATCGCCAGGTGAAGATC H8.5E5T7 H9.5E52.SP6rc
    Hox11_X 8 YQIRELEREFFFSVYINKEKRLQLSRLLNLTDRQVKI------ GTACCAGATCCGAGAGCTGGAGCGAGAATTCTTCTTCAGCGTCTATATCAACAAGGAGAAGCGACTGCAACTCTCGCGTTTGCTCAACTTGACTGACAGGCAGGTCAAGATT H28.5E5T7 H4.5E5T7 H185E5.T7rc H16.5E5T7rc H24.5E5T7rc
    13 Hox13_Z 15 MQLKELEKEYATHKFITKDKRRNISANTGLSERQVTI------ GGCACAACTCAAGGAGCTGGAAAAGGAATACGCGACGCACAAGTTCATCACCAAGGACAAGCGACGAAACATCTCGGCGAACACTGGTCTGAGTGAACGTCAGGTCACCATC H2.5E52.SP6 H3.5E52.SP6 H25.5E52.T7 H7.5E52.SP6
    Hox13_Y 20 MQLGQLEQEYSACKFITKEKRRKIAAAAELSERQVTI------ GATGCAGCTCGGACAGCTGGAGCAGGAGTACAGCGCATGCAAGTTCATCACCAAGGAGAAACGGAGAAAGATTGCCGCAGCAGCCGAGCTGAGTGAGCGCCAGGTCACCATC H20.5E52.T7 H34.5E52.SP6 H36.5E52.SP6 H13.5E52.SP6 H4.5E52.SP6rc H32.5E52.T7rc H35.5E52.SP6rc H29.5E52.T7rc
    GBX ELEKEFHCKKYLSLTERSHIAHALRLSEVQVKIWFQNRR GAGCTGGAAAAAGAGTTCCACTGCAAGAAATACCTGTCGCTCACCGAGCGCTCGCACATCGCCCATGCGCTCCGCTTGAGCGAGGTTCAGGTCAAAATCTGGTTCCAAAATCGCCGCAT H15.T7r H17.T7r H61.T7r H81.T7r H80.T7 H4.sp6 H48.T7 H38r
    Note: The GBX (parahox) sequence is the consensus of all available gbx clones.