New SSR Markers
Mary Polacco
polaccom at missouri.edu
Mon Oct 29 22:10:01 EST 2001
The Maize Mapping Project (MMP) has kindly provided to MaizeDB
information regarding 121 new SSR, with bin map locations for some
117.
A brief summary file follows. Information about the SSR, with links to
external databases may be found at: http://www.agron.missouri.edu/ssr.html
With the new data, there are now 1735 SSR markers in the public sector:
816 have sequence accessions in GenBank.
590 of the accessions are cDNAs,
532 are from the Stanford EST -- Maize Gene Discovery -- Project.
A few, some 23, were mined from EST assemblies computed at TIGR.
Screening images are being loaded this week for the new SSRs.
Map details for previously mapped SSR may now be compared on 3
mapping population using the Compare Maps Utility, listed in the
central box on the MaizeDB homepage. Maps listed in the menu that
display framework SSR markers, together with a handful of RFLPs:
IBM
Tx303xCo159
T218xGT119
To view off-frame markers, please refer to the pdf files
on the SSR summary page: http://www.agron.missouri.edu/ssr.html.
Note: new markers do not appear on these maps.
-Mary Polacco
Curator MaizeDB
PolaccoM at missouri.edu
SSR Bins GenBank PrimerF PrimerR
---------- -------------------- --------------------
------------------------------ ------------------------------
umc2100 1.00 AF264877 AAAGGCATTATGCTCACGTTGATT
TGACGTGCAAACAACCTTCATTAC
umc2183 1.00- 1.01 BG268007 TTAGAGCATGTGGCTCTTAGTCCC
TCTACTGCCAAGAAGAAATCCTGG
umc2157 1.01 BG458447 GACAACGGACGTCAACCATAGC ATCGAAGACCTCAAGGCAAAGTG
umc2096 1.02- 1.03 AF210617 AACGTACCATCCTTGTGCCTGTAT
CATTATTAGTACGGAGCGCTGGTC
umc2185 1.02- 1.03 BG267124 CTTCTTCTGCCACAGCACGAAC
CAAGGTTAAGAGCATGTACGCGAT
umc2191 1.02 BG265983 CAGGTGGTGCAGAGTTTCACAT AAGGTGGAGGATGACTCCAAGAT
umc2097 1.03- 1.04 AF210617 AGATTTGACTGCAAGAAAAGGCTG
GTCCCTCGTCCTGCAAGATTC
umc2124 1.03 AX090093 ATGCGGAGGGGTCTACTACACATA
CTGTGTCTCACTGGAAATGACGAT
umc2145 1.03 AZ918767 GTAGTAGAGGCAGGGCTTCCAAC TAGGAGTTCGTCAGTCAACGAGC
umc2171 1.03- 1.04 BG349843 ACATAATCCCTCGGTACAGGACAA
GCCCTTGTGTGTCTATTTAGGGTG
umc2112 1.04- 1.05 AZ932967 AGCTCTACCAAACACGAGCTTCAT
CAAATGCAGAAAGATAACGCGAAT
umc2083 1.05- 1.06 BF729374 GATGCTCAAGGAGCAGCGAC
CAGGTGGTACGCCATGAACC
umc2151 1.06 AZ918023 ATATGTGGTATTTTCTGCAGGCGT
AAAATCCTATACAGAAAACGGGCG
umc2080 1.08 BF729466 GCCAAGGTGGGTCTGGCTAT ACCACCTTGTCCGTATCCTTCAC
umc2116 1.08 AZ932865 CGGTCGATATAATCTTGGCTGATT
GGCGCAGAGATCATTTGTTTAAT
umc2181 1.08 BG268724 ATCGGGTCCGGATAGATTTTACAC
GTAGCTAGCTTAAGCAGTGCTCCG
umc2149 1.10 AZ918211 TACATGCAAAGCTAGCTAGTCGGA
AGCAGCACCATCGTAATAAGCAC
umc2189 1.10 BG266144 CGTAAGTACAGTACACCAATGGGC
ACACCGACTACAAGCCTCTCAACT
umc2186 2.00- 2.01 BG266921 CTCCCGCAGTCTATGAAGCTCAC
CTCCTCTTCCTCCTCCTCGTTGT
umc2094 2.01 AF223412 TTGGAAAGTTGAGTTGACCTCCAT
ATCTTTGCAAGGTTGAGTTGAAGC
umc2079 2.04 BF729476 CGGCCTCGCTGTCTTCTAGC ATGATCACGTCGTGCTGGTAGTG
umc2088 2.04 BF728075 ACGACAAGAAGGAGGCCAAAG CAAGTAGATCGATCGAGCAGCAG
umc2125 2.04- 2.05 AZ921810 CAAGGGTAAGGGCAAGATGGTAGT
CTGAGGTCTACCTCGGCCATC
umc2110 2.05 BE644336 CTGCGTACTCTAGGTATCCCGTGT
GGTCGGATAGGAGAATCTACAGGC
umc2178 2.06 BG317183 GTATCGAGACACGTACGCACGAA GCGCAGTGATTTCTTACCATGC
umc2129 2.07 AZ921033 ACGTGGTCATCACTCACCGC AAGGAGGAGCGTTCTCGTGG
umc2144 2.07- 2.08 AZ918817 CCAGCCCCTATCTATTTGCTTGT
GAATACTATATCACGGTCGGTCGG
umc2085 2.08 BF729178 TGTACGACTTCTTCTGGACGCAC TAGATGTCGATGTCCTCCAGGG
umc2077 2.09 BF729491 AAACTCACTGAACATGATCCTGGC
CTGGTTCGGATGCAAGTAGTCAG
umc2184 2.09 BG267262 CTTGGCCTACTCCAAGTTCTCG AGTAGAGCAGCACCATCCCG
umc2102 3.00 AF298118 TCATCGATTCATCCATCTCATCTT
ATATTGTATAGTCTGCGGGCTTGA
umc2103 3.00 AF298118 CCTATCCATGCTTGAGGTGTCG GTCCAGGAGGTTGTCGTCCA
umc2104 3.00 AF298118 CTGCTGGCAGTGGCAGTATTC
TACTGCTACACCTTTGTCGTCACC
umc2105 3.00 AF298118 ACATACATAGGCTCCCTTTTTCCG
TCCCGTGACACTCTCTTTCTCTCT
umc2108 3.00 AF298118 CCTTTTAATTTGCAAAGAGAGGTGG
CAAACTAAAGAAAGTCTCGGCAGC
umc2118 3.00 AZ932817 CGTCTCCGTCTGCAGTCACTATTA
TATGGTCCTCGGAGTTTGTTTGTT
umc2071 3.01 AB045772 ACTGATGGTGTTCTTGGGTGTTTT
ATACACGCAGTTACCCGAAGGTT
umc2107 3.01 AF298118 TGAGGTGTGGTAAAAGTGAAAGCA
ATCGATCTCTAGCTGCCTGCCT
umc2117 3.04 AZ932846 GTTTCATGCGTTCCAAATCACAC
GCAGAAGGTCGTCAGTTCTACTCTG
umc2119 3.04 AZ932610 GTCCCAAACAACAAGTGAAGGAAG
GTGTTGTCTGTTGGCTGTTGCT
umc2158 3.04 BG458353 ACACAGCACAACACAACACAACAC
AATAATTGTACCGAGATGTTGGCG
umc2127 3.05 AZ921283 TATTACCTCTCTCCGCAGCTGTA GATGCTTCTTCTCATCACCACTC
umc2155 3.05 BG458661 CATGTGGACACCATAGACCATGA
CCAGAGTTAATGTGACCTAGGCGT
umc2166 3.05 BG410228 TACGTCGTACATCGCCCACC
GTCGTAGCCATATCAGTTGGAACG
umc2076 3.06 BF729528 CTCTCGTCATCTCACCCACTGAAC
CAGCCGTTGGTTACATATTTGGTC
umc2169 3.06 BG354410 ACTACTCCTCGGATAGCCACG GACGAGTAGAGGCTCTGGGAC
umc2081 3.08 BF729464 TTTTTCCACTTGGCTGCTGG
CAGTTTTTCAGAAACGATTTGCCT
umc2174 3.08- 3.09 AX079856 GTACGTACGCAGCCACTTGTCAG
ACATAAATAAAACGTGTGCCGCAG
umc2152 3.09 AZ917975 TAGCTTCACCTGATGATCTTGCAC
CCTTTGTCTTCCGCTATCTTCCTT
umc2148 4.01 AZ918243 GGTAAGTCGTTTCAGCCTTTGCTA
AGACAGAAGAATGCTATGCGGTTC
umc2150 4.02 AZ918175 GTTGTTCACTTTCCAAAACCCTTG
GCCTTGTGCTTCTTGGAGTGTT
umc2082 4.03 BF729461 TAGCTGCCCCTCTTCCGTCT GTCGTGGCGTAGAGACTAGGGAT
umc2176 4.03 BG320129 ATAGATCTTTGTCGCGTGTTCTGC
CTCAAGAACACCACCAGACGAGTT
umc2135 4.08 AZ920497 GTCAGTCAGTCACGAGCTGTTCTC
GCCTCCTTCCGTCGAGAGATA
umc2137 4.08- 4.09 AZ920094 ACCACTGCAACCTAGAGCTGTACC
CACTTGGGTTGTTCCACAGGAG
umc2153 4.08 AZ917952 GCCTTTTTGATTGGTGAATGCT
AGTACGTACAGAACGACTCCAGCC
umc2187 4.08 BG266847 GTCCACCCTACCTCTCAACAAACA
ACCCAACAAGTCTTAATCGGGTTT
umc2188 4.08 BG266818 CGCCAACATGATTAACTTGCTATC
ATTTTCAGTCTGGGTACTTGAGCG
umc2138 4.09 AZ920094 CGGGACAAGGACAGAGCAAG
CAGGGTAAAGCTAGACGGGTAGGTA
umc2139 4.09 AZ920029 ATAAGGAACATCCCCACCTGTTTT
GGTGTGCTGGGTTCTTGTGG
umc2179 5.01 BG316746 TTAACACCTCAAACAGTGATTGCC
GTAGAGCAGCACTCTGGGTTTCTC
umc2115 5.02 AZ932868 CTGTCTGTCTACCCAACCCAACAG
GGGGATAGGCGTGTGTATGTACTG
umc2132 5.02 AZ920939 GAGGCCTCAAATCGCTCTCTG GGTCGTCAGTGAGCTGGTCC
umc2073 5.03 AX048774 GGTGGACGTGTGGTGTGTATATAGTT
GGAGTTGGAGGTGGAGCCTT
umc2113 5.03 AZ932924 CGTACCGTATCTCTCCACGACAG
GTAGGACTGTAGGAGTAGCCGCTG
umc2140 5.03 BG462680 CTAGGGTTTGCCTCTTCCCTCTC
AGTCTAGAGGAAGTCGGAATTGGG
umc2159 5.03 AZ916489 GTTATTTCTGAACCATGGGACTGTG
CTGTATGGGCTCGTATTGTCACCT
umc2161 5.03 AZ916366 ACGGCACACAGATATTTCAGTTCA
AAGATCAGATTTGCTTGTGGGTGT
umc2167 5.03 BG355216 AGACCGGCTAGCGCCATATC AGTGGTGGACGAAGAGACAAGC
umc2086 5.05 BF729035 TGCCAGAGTTCTCGTTACCAA
CGAACAAAAACTTACAGATCCAACA
umc2111 5.05 AW157995 CACGCAACCCACTCATCACTC CTCACCGCTCTGCTCTGCTATC
umc2164 5.05 AZ916225 AGCACACAGACAAGAGAGACAACG
GACCGACAACAGAGATCGAGTACA
umc2072 5.06 AX049377 TGTATTCAGAACGGCTCGTCATAA
GGACGGTTCCGGTTCTAAGATAAG
umc2136 5.08 AZ920322 CCAGATGCGGAAGTAGACGG GATTCGGAGGTGATCTGACCTGT
umc2143 5.08 AZ918879 ACACACAACAGAGCCTTTTGTTCA
AAGAAAAGGACACCAAACCAAACA
umc2074 6.01 AX048762 ACACGGAGATGACAGACGCC
GTTGCCGAAGATGTTGTACTGGAT
umc2141 6.05 AZ919353 ATTAGCACCACCGTGTAGCAAGTT
GGCAGTGTGAGTGGTTGTGTG
umc2123 6.06- 6.07 AX090101 GTGGCGTGTCCTTTCTACGTG
CGAACAGCTAGCTACTGATGATGG
umc2162 6.06 AZ916284 GATGCTGATGACGCTCTACAAGG GACGATGACGAACACCGAGC
umc2170 6.06 BG349861 CACTGCAAGCCTCTACAGACAATG
GAGAGTTCTCCAGGCGAGGTG
umc2165 6.07 AZ916120 AGAACACCAAATGGTGACGTTATGT
CTAGCTCGTCTTCCCTGTGGTCT
umc2109 7.00 AF298118 TGCACGCATTATTGTGTGTACTGA
CCATGGCTTCACTAAAACATCTCC
umc2177 7.00 BG319797 ACCATGCATGTCTCACGTCACT GGGTACGTGCTGTGGAGGAC
umc2160 7.01 AZ916481 TAAAACCTTTACCCCATCCAGCAT
TGTGCTCGTGCTTCTCTCTGAGTA
umc2092 7.02 AX046673 GCACAACCTACTCGCTACCTTACC
ATCGTACTACTCCACTTGCTTGGC
umc2098 7.02 AF244701 GGTGAACAAGATCTCTTTGTCTACTGT
CCTTCTCGGCCATTATTGCT
umc2142 7.02 BG462268 ATGGATCAGGGGAAAGAGCAA CCTCCTCGTCCTCCTTCTTGAT
umc2190 7.06 BG266078 GATCCGTTGAGGTCGATCCTTT
GAGGAGTTCCTGCAGTTTCTTGAC
umc2075 8.03- 8.04 AX048738 CCTGGTATCTTGATGAGCTGGATT
AGAAACATGTCCGGTTCTTCAGAC
umc2146 8.03 AZ918316 GTCTCCGTCCACCTCCTGTG GTCATGGGAATGTGCTGGATG
umc2147 8.03 AZ918316 CTACCCCTACGGCATCACCTACTT
AGACGGAAATGCACCGAGAAG
umc2173 8.03 BG349076 TTCAAAGATCCAGTCAGCAATAAGG
GAACGTGACGCTCTACATGCTG
umc2154 8.04 BG458963 GCTAGTAGTAGTTCCAACGAAGCAACA
GTCACCATCTCCAGGTGCAAGT
umc2182 8.04- 8.05 BG268356 TTCTACCTCCTATCATCGTCCTCG
GAAGAGGAGGAAGTCGACGAGTG
umc2175 8.05- 8.06 BG320980 TACTCCTCGCATTCACATATCGGT
CTTCCTCGTATGGGAAACTTAGCC
umc2089 9.00 BF727920 CAGGAAGAGGAAGAAGGGTCCTC GCCAGCTCTACGGCCTATGAC
umc2131 9.00 AZ920955 CCATAGTAGTGGGGACAGGTTCAT
AGAAACGGCAAATAATGCTGTCAT
umc2078 9.01- 9.02 BF729485 TTTTTGTGCTCGTCTGATTTCTTG
AGACCAATGCAACTCCTACAGACC
umc2084 9.01 BF729356 ATCGCGACGAGTTAATTCAAACAT
TACGATGTCTTCAGTGTGACACCA
umc2093 9.01- 9.02 AF296123 GAAAATGAAGAATAGGAGACATTGTTGC
ATGCACATGCAGTTCCTTGGTTAT
umc2128 9.02- 9.03 AZ921231 CACGGGGAATTCTCATATAGCAAG
GAGTGTGTACGTAGGTATGCCCG
umc2130 9.02 AZ921010 CGAGTTACCTTTGGCACTAGCACT
ATCATGACGTATCTTTCCGAGAGC
umc2087 9.03 BF728356 GTGCTGGCTGAAGAGTTTTACTGG
CTACGGTTAGCTCGCTCGTCTAAG
umc2168 9.03 BG354412 AGAGCCTCTCGGAGATAAGAAGGA
GTGCATACCCACCACCTCGTAG
umc2120 9.04 AZ932600 ACGTCAAGTAGTGAATCCTGCTCC
ATTCTCCGCGGAAGAGACAAG
umc2121 9.04 AZ932511 AAAAGTGGGCGCTAGTACAAGATG
GTGGTGTTCTCCTTTTGATACGCT
umc2095 9.05 AF210618 GTGCTGGTTGTGCATGGTATATTG
CCATGCATGACGCAAGTCTCT
umc2133 9.05 AZ920800 TTCAGGTGTGCACTGACTCTGACT
ATGCTCAAGCTCAACAGCACTTC
umc2134 9.05 AZ920516 TAGTCTAGCGTCGACGAAAAATGC
CAGGCGACGAAGATGAATTGAA
umc2099 9.07 AF244678 AGGTCATCAAGATGCAGAGGGAG TCAAGGTACGAAGCCTGACGAC
umc2114 10.02 AZ932886 ACATGGTTCGTGATATTTTCCCAG
CGTCGTTCACCACAATAATGAGAA
umc2180 10.03 BG316573 ATCAGCATCGATAGCGAAGAAAGA
ATTGCTACTAGGGTTGTTGTTGCC
umc2156 10.04-10.05 BG458572 ACGACGGCAAGAAGAAAACTACTG
CGACCTGCTTTCAGTCTCTCTAGC
umc2163 10.04 AZ916248 AAGCGGGAATCTGAATCTTTGTTC
GAAATTGCTGGGGTTCTCATTTCT
umc2122 10.07 AF326509 TTGACAAGCTAGTGTGCAACTGTG
TGAAAGCCCACTGGACAAACTAAT
umc2126 10.07 AZ921783 CAGTTCTGCACTTCTGCTTGCTC AGGACTGTGAAGAGCGCGAG
umc2172 10.07 BG349450 AGTAATCTCATGCCCGCTCTTCTT
TACGCTGAGTCAAAAACCAGGAAT
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