Table 1 |
|||||||||||
|
SNP identified in LAP3, LCORL, and NCAPG genes in crossbred steers. |
|||||||||||
|
Gene 1 |
Marker Name2 |
Accession Number |
dbSTS _Id |
ss # |
SNP3 |
Position in Gene4 |
Location on BTA65 |
For Primer Name |
For Primer Seq |
Rev Primer Name |
Rev Primer Seq |
|
|
|||||||||||
|
LAP3 |
79140_312 |
GF102128 |
1233209 |
196003657 |
INDEL |
p.E47del |
37964162 |
LAP3-EX2F |
GCCTTGTTCTTTTGTCCTTGAG |
LAP3-EX2R |
TTGGGTTGAAGTAGCCTGATTT |
|
LAP3 |
79144_139 |
GF102139 |
1233220 |
196003658 |
S |
p.D92E |
37966065 |
LAP3-EX4F |
ACCAAATTTCTTGGGGAGTTTT |
LAP3-EX4R |
AACACTGCAAGAGGGAACAAAT |
|
LAP3 |
79146_218 |
GF102161 |
1233242 |
196003659 |
Y |
c.504C>T |
37967629 |
LAP3-EX5F |
GGGAAGAAGTGAAAGCTCAGAA |
LAP3-EX5R |
AAACTGACTAGGGCCATGAGAG |
|
LAP3 |
79150_94 |
GF102129 |
1233210 |
196003660 |
Y |
c.834C>T |
37971945 |
LAP3-EX7F |
CATTTTTCATTTCCTGCCTTGT |
LAP3-EX7R |
GTAAGCAAAGGGAAGACAGCAT |
|
LAP3 |
79152_265 |
GF102108 |
1233189 |
196003661 |
Y |
37977863 |
LAP3-EX8F |
TGGAAATTTCTTGGTGCTTGTA |
LAP3-EX8R |
CTGACTGCTAACCACATTTTGC |
|
|
LAP3 |
79154_194 |
GF102068 |
1233149 |
196003662 |
Y |
37979109 |
LAP3-EX9F |
CACACTCCATGTTCCTTCATGT |
LAP3-EX9R |
TGCAGGACTTGTTTTCTTCTCA |
|
|
LAP3 |
79154_347 |
GF102068 |
1233149 |
196003663 |
S |
37979262 |
LAP3-EX9F |
CACACTCCATGTTCCTTCATGT |
LAP3-EX9R |
TGCAGGACTTGTTTTCTTCTCA |
|
|
LAP3 |
79158_103 |
GF102082 |
1233163 |
196003664 |
S |
37984197 |
LAP3-EX11F |
AGGATTTGCCAACATCATCTTT |
LAP3-EX11R |
CCATGCCTTCTTTTACAAAGCTA |
|
|
LAP3 |
79158_104 |
GF102082 |
1233163 |
196003665 |
R |
37984198 |
LAP3-EX11F |
AGGATTTGCCAACATCATCTTT |
LAP3-EX11R |
CCATGCCTTCTTTTACAAAGCTA |
|
|
LAP3 |
79160_105 |
GF102096 |
1233177 |
196003666 |
Y |
37985986 |
LAP3-EX12F |
ATTTCAGCAAATGCCCTACAAT |
LAP3-EX12R |
TTGAAAATGCAAAAACCAGTTG |
|
|
LAP3 |
79162_241 |
GF102069 |
1233150 |
196003667 |
K |
c.*1641T>G |
37986804 |
LAP3-EX13F |
TGGGGTTAGATGTTGATTTTTG |
LAP3-EX13R |
GTGAATATGAGAGCCACACCAG |
|
LAP3 |
79162_246 |
GF102069 |
1233150 |
196003668 |
Y |
c.*1646C>T |
37986809 |
LAP3-EX13F |
TGGGGTTAGATGTTGATTTTTG |
LAP3-EX13R |
GTGAATATGAGAGCCACACCAG |
|
LAP3 |
79162_438 |
GF102069 |
1233150 |
196003669 |
R |
c.*1838A>G |
37987001 |
LAP3-EX13F |
TGGGGTTAGATGTTGATTTTTG |
LAP3-EX13R |
GTGAATATGAGAGCCACACCAG |
|
|
|||||||||||
|
NCAPG |
83704_234 |
GF110810 |
1241907 |
263198259 |
R |
38157198 |
NCAPG-EX4-F |
TCTGTCCTTTTCAAGGGATGTT |
NCAPG-EX4-R |
CAGCCACACAATAATGCGATAG |
|
|
NCAPG |
83704_335 |
GF110810 |
1241907 |
263198262 |
S |
38157299 |
NCAPG-EX4-F |
TCTGTCCTTTTCAAGGGATGTT |
NCAPG-EX4-R |
CAGCCACACAATAATGCGATAG |
|
|
NCAPG |
83704_358 |
GF110810 |
1241907 |
263198260 |
W |
38157322 |
NCAPG-EX4-F |
TCTGTCCTTTTCAAGGGATGTT |
NCAPG-EX4-R |
CAGCCACACAATAATGCGATAG |
|
|
NCAPG |
83704_366 |
GF110810 |
1241907 |
263198261 |
R |
38157330 |
NCAPG-EX4-F |
TCTGTCCTTTTCAAGGGATGTT |
NCAPG-EX4-R |
CAGCCACACAATAATGCGATAG |
|
|
NCAPG |
83708_361 |
GF110811 |
1241908 |
263198263 |
Y |
38158932 |
NCAPG-EX6-F |
GATGGAAGCTAGAGGGGAACTT |
NCAPG-EX6-R |
CTTTTCATGGTAGGCCTAATGC |
|
|
NCAPG |
83712_168 |
GF110812 |
1241909 |
263198264 |
R |
c.1261A>G |
38163729 |
NCAPG-EX8-F |
TTCTCACTTAATGGGGAGCTGT |
NCAPG-EX8-R |
AAATTTTAAGCAAAAACCTGCAA |
|
NCAPG |
83712_422 |
GF110812 |
1241909 |
263198265 |
R |
38163983 |
NCAPG-EX8-F |
TTCTCACTTAATGGGGAGCTGT |
NCAPG-EX8-R |
AAATTTTAAGCAAAAACCTGCAA |
|
|
NCAPG |
83714_209 |
GF110813 |
1241910 |
263198266 |
M |
c.1357A>C |
38164388 |
NCAPG-EX9-F |
TTTCAGAATGTGAATTTTGGCTTA |
NCAPG-EX9-R |
GTGTGAAAGGGACTGGGTTTTA |
|
NCAPG |
83714_224 |
GF110813 |
1241910 |
263198267 |
K |
p.I442M |
38164403 |
NCAPG-EX9-F |
TTTCAGAATGTGAATTTTGGCTTA |
NCAPG-EX9-R |
GTGTGAAAGGGACTGGGTTTTA |
|
NCAPG |
83724_658 |
GF110818 |
1241915 |
263198273 |
Y |
c.2158T>C |
38180790 |
NCAPG-EX14-F |
ATTTACTTTTGGTGGGGGATGT |
NCAPG-EX14-R |
CAACCTCCCAATAGTCATTTCA |
|
NCAPG |
83726_315 |
GF110815 |
1241912 |
263198269 |
R |
38192653 |
NCAPG-EX15-F |
ATGTAAGGCCTAAAAGGGAGGT |
NCAPG-EX15-R |
GGAAAGAGCCAAATAATTCAGG |
|
|
NCAPG |
83730_778 |
GF110816 |
1241913 |
263198270 |
M |
p.L877M |
38195339 |
NCAPG-EX17-F |
GAGCGTGAATGGTTCAGTACAC |
NCAPG-EX17-R |
ACTTCAAGAAATGAGCACCAAA |
|
NCAPG |
83732_316 |
GF110819 |
1241916 |
263198271 |
R |
38195743 |
NCAPG-EX18-F |
AGTATTTGGTGCTCATTTCTTGA |
NCAPG-EX18-R |
TCCCAAGTGAATTTAATTAGAAAAA |
|
|
|
|||||||||||
|
LCORL |
79205_443 |
GF102113 |
1233194 |
196003679 |
R |
38233294 |
LOC540095-EX6F |
CCTATGTAGTGCCTTCCCAGTC |
LOC540095-EX6R |
CTCGTCCTGCTTCTTAGTTTGT |
|
|
LCORL |
81441_243 |
GF102084 |
1233165 |
196003694 |
Y |
38255270 |
LOC540095-IN4.4F |
GCATGAATGACAAAACTGTGCT |
LOC540095-IN4.4R |
CATTTTGCCCTTAAGCCTTCTA |
|
|
LCORL |
81439_210 |
GF102101 |
1233182 |
196003693 |
R |
38257174 |
LOC540095-IN4.3F |
TTTGCCTTCAGTTCTCTTAGGC |
LOC540095-IN4.3R |
TTGCAAAATTATGGCATTTCAC |
|
|
LCORL |
81435_188 |
GF102143 |
1233224 |
196003692 |
Y |
38284737 |
LOC540095-IN4.1F |
TAGCCTGACTGCATCCATCTAA |
LOC540095-IN4.1R |
GGAAATCCCTGGTTAAGAATCC |
|
|
LCORL |
79197_655 |
GF110814 |
1241911 |
263198268 |
R |
38327100 |
LOC540095-EX2F |
TCTCACGTAGAGTGTATGGATAAGC |
LOC540095-EX2R |
GAGTTCCAGGCTGCCTATATCA |
|
|
LCORL |
81433_176 |
GF110817 |
1241914 |
263198272 |
Y |
38314844 |
LOC540095-IN3.1F |
GCAGGTGAAAATCCCAATACAC |
LOC540095-IN3.1R |
GGGCCAAACTAGCCTTATTTCT |
|
|
LCORL |
81419_461 |
GF102100 |
1233181 |
196003691 |
M |
38342145 |
LOC540095-IN1.9F |
GACTTCAAATTTTTGCCCAGAG |
LOC540095-IN1.9R |
GGTGTTCTTACCCTGTCTCAGC |
|
|
LCORL |
81413_159 |
GF102115 |
1233196 |
196003686 |
S |
38359337 |
LOC540095-IN1.6F |
AGGATCAACCATTAGGATGTGC |
LOC540095-IN1.6R |
AACTGGGAAGAGAGCAAGTGAG |
|
|
LCORL |
81413_221 |
GF102115 |
1233196 |
196003684 |
W |
38359399 |
LOC540095-IN1.6F |
AGGATCAACCATTAGGATGTGC |
LOC540095-IN1.6R |
AACTGGGAAGAGAGCAAGTGAG |
|
|
LCORL |
81413_226 |
GF102115 |
1233196 |
196003687 |
W |
38359404 |
LOC540095-IN1.6F |
AGGATCAACCATTAGGATGTGC |
LOC540095-IN1.6R |
AACTGGGAAGAGAGCAAGTGAG |
|
|
LCORL |
81413_231 |
GF102115 |
1233196 |
196003689 |
M |
38359409 |
LOC540095-IN1.6F |
AGGATCAACCATTAGGATGTGC |
LOC540095-IN1.6R |
AACTGGGAAGAGAGCAAGTGAG |
|
|
LCORL |
81413_238 |
GF102115 |
1233196 |
196003690 |
W |
38359416 |
LOC540095-IN1.6F |
AGGATCAACCATTAGGATGTGC |
LOC540095-IN1.6R |
AACTGGGAAGAGAGCAAGTGAG |
|
|
LCORL |
81405_282 |
GF102099 |
1233180 |
196003685 |
M |
38376731 |
LOC540095-IN1.2F |
TCGGGTCCTCTTTTACTGTCAT |
LOC540095-IN1.2R |
CTTACCACGATCTCCTTTCCAC |
|
|
|
|||||||||||
|
1 SNP in bold were genotyped using the Sequenom MassArray System. 2 Marker name in USMARC database. 3 IUB Codes for SNP are K = G/T, M = A/C, R = A/G, S = C/G, W = A/T, Y = C/T. 4 Position based on NM_174098 Bos taurus leucine aminopeptidase 3 (LAP3) mRNA; NM_001102376 Bos taurus non-SMC condensin I complex, subunit G (NCAPG), mRNA; and NM_001192357 Bos taurus ligand dependent nuclear receptor corepressor-like (LCORL) mRNA. 5 Position based on the Btau 4.0 genome assembly. |
|||||||||||
|
Lindholm-Perry et al. BMC Genetics 2011 12:103 doi:10.1186/1471-2156-12-103 |
|||||||||||
