GT54 M04
NM_145926
LOCUS NM_145926 1678 bp mRNA linear ROD 27-OCT-2004
DEFINITION Mus musculus mannoside acetylglucosaminyltransferase 4, isoenzyme B
(Mgat4b), mRNA.
ACCESSION NM_145926
VERSION NM_145926.2 GI:33239191
KEYWORDS .
SOURCE Mus musculus (house mouse)
ORGANISM Mus musculus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
REFERENCE 1 (bases 1 to 1678)
AUTHORS Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D.,
Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K.,
Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F.,
Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L.,
Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J.,
Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A.,
Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S.,
Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y.,
Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D.,
Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M.,
Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E.,
Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
TITLE Generation and initial analysis of more than 15,000 full-length
human and mouse cDNA sequences
JOURNAL Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002)
PUBMED 12477932
COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final
NCBI review. The reference sequence was derived from AB053218.1.
On Jul 25, 2003 this sequence version replaced gi:22122340.
FEATURES Location/Qualifiers
source 1..1678
/organism="Mus musculus"
/mol_type="mRNA"
/db_xref="taxon:10090"
/chromosome="11"
gene 1..1678
/gene="Mgat4b"
/db_xref="GeneID:103534"
/db_xref="LocusID:103534"
/db_xref="MGI:2143974"
CDS 11..1657
/gene="Mgat4b"
/note="mannosyl (alpha-1,3-)-glycoprotein
beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B;
go_function: transferase activity [goid 0016740] [evidence
IEA];
go_function: transferase activity, transferring glycosyl
groups [goid 0016757] [evidence IEA]"
/codon_start=1
/product="N-acetylglucosaminyltransferase IVb"
/protein_id="NP_666038.2"
/db_xref="GI:33239192"
/db_xref="GeneID:103534"
/db_xref="LocusID:103534"
/db_xref="MGI:2143974"
/translation="MRLRNGTFLTLLLFCLCAFLSLSWYAALSGQKGDVVDIYQREFL
ALRDRLHAAEQESLKRSKELNLVLEEIKRAVSERQALRDGEGNRTWGRLTEDPRLKPW
NVSHRHVLHLPTVFHHLPHLLAKESSLQPAVRVGQGRTGVSVVMGIPSVRREVHSYLT
DTLHSLISELSPQEKEDSVIVVLIAETDPQYTSAVTENIKALFPTEIHSGLLEVISPS
PHFYPDFSRLRESFGDPKERVRWRTKQNLDYCFLMMYAQSKGIYYVQLEDDIVAKPNY
LSTMKNFALQQPSEDWMILEFSQLGFIGKMFKSLDLSLIVEFILMFYRDKPIDWLLDH
ILWVKVCNPEKDAKHCDRQKANLRIRFKPSLFQHVGTHSSLAGKIQKLKDKDFGKHAL
RKSYVNPPAEVSTSLKTYQHFTLEKAYLREDFFWAFTPAAGDFIRFRFFQPLRLERFF
FRSGNIEHPEDKLFNTSVEVLPFDNPQSEKEALQEGRSATLRYPRSPDGYLQIGSFYK
GVAEGEVDPAFGPLEALRLSIQTDSPVWVILSEIFLKKAD"
ORIGIN
1 atcgggggag atgaggctcc gcaatggcac cttcctgacg ctgctgctct tctgcttgtg
61 cgccttcctc tcgctctcct ggtacgcagc gctcagcggc cagaaaggtg acgtggtgga
121 catttaccag cgcgagttcc tggctctgcg agaccgtttg cacgcggctg agcaagagag
181 cctgaagcgc tccaaggagc taaacctggt gctggaagaa atcaagaggg cagtatccga
241 gaggcaagcg ctgcgggacg gagaaggcaa tcgcacttgg ggccgcctaa cagaggatcc
301 gcgactgaag ccgtggaacg tctcgcacag gcacgtactt catctgccca ccgtcttcca
361 ccatctgccg cacctgctgg ctaaggagag cagtctgcag cccgcagtgc gagtgggcca
421 gggccgcacc ggagtatccg tggtgatggg cattccgagc gtacggcgcg aggtgcactc
481 gtacttgact gacacattgc actcgctcat ctcggagctg agcccgcagg agaaggaaga
541 ctcagtcatc gtggtgctga tcgccgagac tgacccacag tacacttcgg cagtgacaga
601 gaacatcaag gccttgttcc ccacagagat ccattctggg ctcctggaag tcatctcccc
661 ttcccctcac ttctaccctg acttctcccg ccttcgagag tcctttgggg accccaagga
721 gagagtcagg tggaggacca aacagaacct cgattactgc ttcctcatga tgtatgcaca
781 gtccaaaggc atctactatg tgcagctgga ggatgacatt gtagccaagc ccaactactt
841 gagcactatg aagaactttg ccctccagca gccctccgag gactggatga tcctggagtt
901 ctcgcagttg ggcttcattg ggaagatgtt caagtcactg gatctgagcc tgattgtgga
961 gttcatcctc atgttctacc gggacaagcc catagactgg ctcctggacc acatcctgtg
1021 ggtgaaagtc tgcaaccctg agaaggatgc gaaacattgt gatcggcaga aggccaacct
1081 tcggatccgc ttcaagccgt cccttttcca gcatgtgggc actcactcat cactggcggg
1141 caaaatccag aaactgaagg ataaagactt tggaaagcat gctctccgga agagctacgt
1201 gaacccaccg gcagaggtga gcacaagcct caagacgtac cagcatttca ccctggagaa
1261 ggcctacttg cgggaggatt tcttctgggc cttcacacct gccgcaggag actttatccg
1321 gttccgcttc ttccagccac tgcgccttga gcggttcttc ttccgaagcg ggaacatcga
1381 gcacccggaa gataagctct tcaacacttc tgtggaggtg ctgccctttg ataaccccca
1441 gtcagagaag gaggcccttc aggaaggccg ctcagccact ctccggtacc ctaggagccc
1501 agatggatac ctccagattg gctccttcta caagggtgta gctgaaggag aagtggatcc
1561 tgcctttggc cccctggaag cactacgtct ctccattcag actgactccc cggtgtgggt
1621 cattttgagt gagatctttc tgaaaaaggc cgactagaag gcttccaagg gtgctc
Coding Region:
1 atgaggctcc gcaatggcac cttcctgacg ctgctgctct tctgcttgtg cgccttcctc
61 tcgctctcct ggtacgcagc gctcagcggc cagaaaggtg acgtggtgga catttaccag
121 cgcgagttcc tggctctgcg agaccgtttg cacgcggctg agcaagagag cctgaagcgc
181 tccaaggagc taaacctggt gctggaagaa atcaagaggg cagtatccga gaggcaagcg
241 ctgcgggacg gagaaggcaa tcgcacttgg ggccgcctaa cagaggatcc gcgactgaag
301 ccgtggaacg tctcgcacag gcacgtactt catctgccca ccgtcttcca ccatctgccg
361 cacctgctgg ctaaggagag cagtctgcag cccgcagtgc gagtgggcca gggccgcacc
421 ggagtatccg tggtgatggg cattccgagc gtacggcgcg aggtgcactc gtacttgact
481 gacacattgc actcgctcat ctcggagctg agcccgcagg agaaggaaga ctcagtcatc
541 gtggtgctga tcgccgagac tgacccacag tacacttcgg cagtgacaga gaacatcaag
601 gccttgttcc ccacagagat ccattctggg ctcctggaag tcatctcccc ttcccctcac
661 ttctaccctg acttctcccg ccttcgagag tcctttgggg accccaagga gagagtcagg
721 tggaggacca aacagaacct cgattactgc ttcctcatga tgtatgcaca gtccaaaggc
781 atctactatg tgcagctgga ggatgacatt gtagccaagc ccaactactt gagcactatg
841 aagaactttg ccctccagca gccctccgag gactggatga tcctggagtt ctcgcagttg
901 ggcttcattg ggaagatgtt caagtcactg gatctgagcc tgattgtgga gttcatcctc
961 atgttctacc gggacaagcc catagactgg ctcctggacc acatcctgtg ggtgaaagtc
1021 tgcaaccctg agaaggatgc gaaacattgt gatcggcaga aggccaacct tcggatccgc
1081 ttcaagccgt cccttttcca gcatgtgggc actcactcat cactggcggg caaaatccag
1141 aaactgaagg ataaagactt tggaaagcat gctctccgga agagctacgt gaacccaccg
1201 gcagaggtga gcacaagcct caagacgtac cagcatttca ccctggagaa ggcctacttg
1261 cgggaggatt tcttctgggc cttcacacct gccgcaggag actttatccg gttccgcttc
1321 ttccagccac tgcgccttga gcggttcttc ttccgaagcg ggaacatcga gcacccggaa
1381 gataagctct tcaacacttc tgtggaggtg ctgccctttg ataaccccca gtcagagaag
1441 gaggcccttc aggaaggccg ctcagccact ctccggtacc ctaggagccc agatggatac
1501 ctccagattg gctccttcta caagggtgta gctgaaggag aagtggatcc tgcctttggc
1561 cccctggaag cactacgtct ctccattcag actgactccc cggtgtgggt cattttgagt
1621 gagatctttc tgaaaaaggc cgactag
Celera Report:
/organism=Mus musculus /order=11
/ga_uid=232000009821448 /len=12454175 /scaffold_class=ge10k
Length = 500000
Score = 373 bits (188), Expect = e-100
Identities = 188/188 (100%)
Strand = Plus / Minus
Query: 96 aggtgacgtggtggacatttaccagcgcgagttcctggctctgcgagaccgtttgcacgc 155
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205933 aggtgacgtggtggacatttaccagcgcgagttcctggctctgcgagaccgtttgcacgc 205874
Query: 156 ggctgagcaagagagcctgaagcgctccaaggagctaaacctggtgctggaagaaatcaa 215
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205873 ggctgagcaagagagcctgaagcgctccaaggagctaaacctggtgctggaagaaatcaa 205814
Query: 216 gagggcagtatccgagaggcaagcgctgcgggacggagaaggcaatcgcacttggggccg 275
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205813 gagggcagtatccgagaggcaagcgctgcgggacggagaaggcaatcgcacttggggccg 205754
Query: 276 cctaacag 283
||||||||
Sbjct: 205753 cctaacag 205746
Score = 363 bits (183), Expect = 2e-97
Identities = 197/199 (98%), Gaps = 2/199 (1%)
Strand = Plus / Minus
Query: 1148 aggataaagactttggaaagcatgctctccggaag-agctacgtgaacccaccggcagag 1206
||||||||||||||||||||||||||||||||||| ||| ||||||||||||||||||||
Sbjct: 203149 aggataaagactttggaaagcatgctctccggaaggagc-acgtgaacccaccggcagag 203091
Query: 1207 gtgagcacaagcctcaagacgtaccagcatttcaccctggagaaggcctacttgcgggag 1266
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203090 gtgagcacaagcctcaagacgtaccagcatttcaccctggagaaggcctacttgcgggag 203031
Query: 1267 gatttcttctgggccttcacacctgccgcaggagactttatccggttccgcttcttccag 1326
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203030 gatttcttctgggccttcacacctgccgcaggagactttatccggttccgcttcttccag 202971
Query: 1327 ccactgcgccttgagcggt 1345
|||||||||||||||||||
Sbjct: 202970 ccactgcgccttgagcggt 202952
Score = 285 bits (144), Expect = 4e-74
Identities = 144/144 (100%)
Strand = Plus / Minus
Query: 281 cagaggatccgcgactgaagccgtggaacgtctcgcacaggcacgtacttcatctgccca 340
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205653 cagaggatccgcgactgaagccgtggaacgtctcgcacaggcacgtacttcatctgccca 205594
Query: 341 ccgtcttccaccatctgccgcacctgctggctaaggagagcagtctgcagcccgcagtgc 400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205593 ccgtcttccaccatctgccgcacctgctggctaaggagagcagtctgcagcccgcagtgc 205534
Query: 401 gagtgggccagggccgcaccggag 424
||||||||||||||||||||||||
Sbjct: 205533 gagtgggccagggccgcaccggag 205510
Score = 270 bits (136), Expect = 2e-69
Identities = 136/136 (100%)
Strand = Plus / Minus
Query: 423 agtatccgtggtgatgggcattccgagcgtacggcgcgaggtgcactcgtacttgactga 482
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205422 agtatccgtggtgatgggcattccgagcgtacggcgcgaggtgcactcgtacttgactga 205363
Query: 483 cacattgcactcgctcatctcggagctgagcccgcaggagaaggaagactcagtcatcgt 542
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205362 cacattgcactcgctcatctcggagctgagcccgcaggagaaggaagactcagtcatcgt 205303
Query: 543 ggtgctgatcgccgag 558
||||||||||||||||
Sbjct: 205302 ggtgctgatcgccgag 205287
Score = 262 bits (132), Expect = 6e-67
Identities = 132/132 (100%)
Strand = Plus / Minus
Query: 910 gggaagatgttcaagtcactggatctgagcctgattgtggagttcatcctcatgttctac 969
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203667 gggaagatgttcaagtcactggatctgagcctgattgtggagttcatcctcatgttctac 203608
Query: 970 cgggacaagcccatagactggctcctggaccacatcctgtgggtgaaagtctgcaaccct 1029
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203607 cgggacaagcccatagactggctcctggaccacatcctgtgggtgaaagtctgcaaccct 203548
Query: 1030 gagaaggatgcg 1041
||||||||||||
Sbjct: 203547 gagaaggatgcg 203536
Score = 240 bits (121), Expect = 2e-60
Identities = 121/121 (100%)
Strand = Plus / Minus
Query: 791 tgcagctggaggatgacattgtagccaagcccaactacttgagcactatgaagaactttg 850
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204052 tgcagctggaggatgacattgtagccaagcccaactacttgagcactatgaagaactttg 203993
Query: 851 ccctccagcagccctccgaggactggatgatcctggagttctcgcagttgggcttcattg 910
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203992 ccctccagcagccctccgaggactggatgatcctggagttctcgcagttgggcttcattg 203933
Query: 911 g 911
|
Sbjct: 203932 g 203932
Score = 230 bits (116), Expect = 2e-57
Identities = 116/116 (100%)
Strand = Plus / Minus
Query: 606 gttccccacagagatccattctgggctcctggaagtcatctccccttcccctcacttcta 665
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204587 gttccccacagagatccattctgggctcctggaagtcatctccccttcccctcacttcta 204528
Query: 666 ccctgacttctcccgccttcgagagtcctttggggaccccaaggagagagtcaggt 721
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204527 ccctgacttctcccgccttcgagagtcctttggggaccccaaggagagagtcaggt 204472
Score = 218 bits (110), Expect = 8e-54
Identities = 110/110 (100%)
Strand = Plus / Minus
Query: 1041 gaaacattgtgatcggcagaaggccaaccttcggatccgcttcaagccgtcccttttcca 1100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203336 gaaacattgtgatcggcagaaggccaaccttcggatccgcttcaagccgtcccttttcca 203277
Query: 1101 gcatgtgggcactcactcatcactggcgggcaaaatccagaaactgaagg 1150
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 203276 gcatgtgggcactcactcatcactggcgggcaaaatccagaaactgaagg 203227
Score = 212 bits (107), Expect = 5e-52
Identities = 114/115 (99%), Gaps = 1/115 (0%)
Strand = Plus / Minus
Query: 1510 ggctccttctacaagggtgtagctgaaggagaagtggatcctgcctttggccccctggaa 1569
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 202202 ggctccttctacaagggtgtagctgaaggagaagtggatcctgcctttggccccctggaa 202143
Query: 1570 gcactacgtctctccattcagactgac-tccccggtgtgggtcattttgagtgag 1623
||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Sbjct: 202142 gcactacgtctctccattcagactgacttccccggtgtgggtcattttgagtgag 202088
Score = 200 bits (101), Expect = 2e-48
Identities = 101/101 (100%)
Strand = Plus / Minus
Query: 1 atgaggctccgcaatggcaccttcctgacgctgctgctcttctgcttgtgcgccttcctc 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 210968 atgaggctccgcaatggcaccttcctgacgctgctgctcttctgcttgtgcgccttcctc 210909
Query: 61 tcgctctcctggtacgcagcgctcagcggccagaaaggtga 101
|||||||||||||||||||||||||||||||||||||||||
Sbjct: 210908 tcgctctcctggtacgcagcgctcagcggccagaaaggtga 210868
Score = 176 bits (89), Expect = 3e-41
Identities = 89/89 (100%)
Strand = Plus / Minus
Query: 1423 aacccccagtcagagaaggaggcccttcaggaaggccgctcagccactctccggtaccct 1482
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 202367 aacccccagtcagagaaggaggcccttcaggaaggccgctcagccactctccggtaccct 202308
Query: 1483 aggagcccagatggatacctccagattgg 1511
|||||||||||||||||||||||||||||
Sbjct: 202307 aggagcccagatggatacctccagattgg 202279
Score = 159 bits (80), Expect = 7e-36
Identities = 80/80 (100%)
Strand = Plus / Minus
Query: 1343 ggttcttcttccgaagcgggaacatcgagcacccggaagataagctcttcaacacttctg 1402
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 202529 ggttcttcttccgaagcgggaacatcgagcacccggaagataagctcttcaacacttctg 202470
Query: 1403 tggaggtgctgccctttgat 1422
||||||||||||||||||||
Sbjct: 202469 tggaggtgctgccctttgat 202450
Score = 157 bits (79), Expect = 3e-35
Identities = 79/79 (100%)
Strand = Plus / Minus
Query: 717 caggtggaggaccaaacagaacctcgattactgcttcctcatgatgtatgcacagtccaa 776
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204307 caggtggaggaccaaacagaacctcgattactgcttcctcatgatgtatgcacagtccaa 204248
Query: 777 aggcatctactatgtgcag 795
|||||||||||||||||||
Sbjct: 204247 aggcatctactatgtgcag 204229
Score = 101 bits (51), Expect = 1e-18
Identities = 51/51 (100%)
Strand = Plus / Minus
Query: 557 agactgacccacagtacacttcggcagtgacagagaacatcaaggccttgt 607
|||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204874 agactgacccacagtacacttcggcagtgacagagaacatcaaggccttgt 204824
Score = 52.0 bits (26), Expect = 0.001
Identities = 26/26 (100%)
Strand = Plus / Minus
Query: 1622 agatctttctgaaaaaggccgactag 1647
||||||||||||||||||||||||||
Sbjct: 202006 agatctttctgaaaaaggccgactag 201981
Primer3 Output
WARNING: Numbers in input sequence were deleted.
PRIMER PICKING RESULTS FOR gt54 m54
No mispriming library specified
Using 1-based sequence positions
OLIGO start len tm gc% any 3'seq
LEFT PRIMER 1 20 60.28 50.00 4.00 2.00 aggtgacgtggtggacattt
RIGHT PRIMER 83 20 60.97 55.00 3.00 2.00 gcttcaggctctcttgctca
SEQUENCE SIZE: 188
INCLUDED REGION SIZE: 188
PRODUCT SIZE: 83, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 1.00
1 aggtgacgtggtggacatttaccagcgcgagttcctggctctgcgagaccgtttgcacgc
>
61 ggctgagcaagagagcctgaagcgctccaaggagctaaacctggtgctggaagaaatcaa
<
121 gagggcagtatccgagaggcaagcgctgcgggacggagaaggcaatcgcacttggggccg
181 cctaacag
KEYS (in order of precedence):
> left primer
< right primer
ADDITIONAL OLIGOS
start len tm gc% any 3'seq
1 LEFT PRIMER 1 20 60.28 50.00 4.00 2.00 aggtgacgtggtggacattt
RIGHT PRIMER 81 20 60.97 55.00 5.00 5.00 ttcaggctctcttgctcagc
PRODUCT SIZE: 81, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 0.00
2 LEFT PRIMER 93 20 59.88 50.00 5.00 0.00 agctaaacctggtgctggaa
RIGHT PRIMER 173 19 60.36 52.63 6.00 0.00 aagtgcgattgccttctcc
PRODUCT SIZE: 81, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 2.00
3 LEFT PRIMER 94 20 59.88 55.00 5.00 1.00 gctaaacctggtgctggaag
RIGHT PRIMER 173 19 60.36 52.63 6.00 0.00 aagtgcgattgccttctcc
PRODUCT SIZE: 80, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00
4 LEFT PRIMER 93 20 59.88 50.00 5.00 0.00 agctaaacctggtgctggaa
RIGHT PRIMER 174 19 59.54 52.63 6.00 2.00 caagtgcgattgccttctc
PRODUCT SIZE: 82, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 2.00
Statistics
con too in in no tm tm high high high
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 332 0 0 0 0 0 71 212 0 0 0 7 42
Right 309 0 0 0 0 0 68 182 1 0 14 6 38
Pair Stats:
considered 729, unacceptable product size 705, tm diff too large 7, high any compl 4, ok 13
primer3 release 1.0
(primer3_www_results.cgi v 0.
Primers to test: OK in Blast searches
OLIGO start len tm gc% any 3'seq
LEFT PRIMER 1 20 60.28 50.00 4.00 2.00 aggtgacgtggtggacattt
RIGHT PRIMER 83 20 60.97 55.00 3.00 2.00 gcttcaggctctcttgctca
SEQUENCE SIZE: 188
INCLUDED REGION SIZE: 188
PRODUCT SIZE: 83, PAIR ANY COMPL: 3.00, PAIR 3' COMPL: 1.00
Molecular Beacon:
Molecular Beacon Primer Design Protocol
- Enter exon sequence.
- Restrict primer temperature to 59-61ºC.
- Restrict primer length to 19-21 base pairs.
- Change the following parameters:
- Hairpin Max Delta G (3’end) - 2 kcal/mol
- Hairpin Max Delta G (Internal) - 3 kcal/mol
- 3’ end max delta G - 10 kcal/mol
- Self Dimer Max Delta G (3’end) - 5 kcal/mol
- Self Dimer Max Delta G (Internal) -6 kcal/mol
- Run/Repeat (dinucl.) Max Length -3 bp
- G/C clamp-Target consec. G/C’s at 3’ end – 1
- Amplicon Length – 65-75 base pairs
- Max Ambiguous Bases in Amplicon – 0
- Max Primer Pair Tm Mismatch – 1C
- Cross Dimer Max Delta G (3’ end) – 5 kcal/mol
- Cross Dimer Max Delta G (Internal) – 6 kcal/mol
- %GC Content – N/A
VALIDATED PRIMER SEQUENCES:
FORWARD PRIMER:AGGTGACGTGGTGGACATTT
REVERSE PRIMER:GCTTCAGGCTCTCTTGCTCA