Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8823
Trapped Gene
Man2a1 (ENSMUSG00000024085)
Vector Insertion
Chr 17: 64985996 - 65000535
Public Clones TEA128 (baygenomics)
Private Clones OST432549 (lexicon)
Severity of mutation (?) Insertion after 20% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000495787 (Chr17:64985824..64985995 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCTTGCAAAATGGTGGGATA Chr17:64985942..64985961 60.69 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000495787 (Chr17:64985824..64985995 +)
Downstram Exon
ENSMUSE00000493264 (Chr17:65000536..65000663 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCTTGCAAAATGGTGGGATA Chr17:64985942..64985961 60.69 45 TGGCTTCATCAGGCATAACC Chr17:65000600..65000619 61 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000483264 Chr17:64950989..64951210 GCGATCTTCTGCGTCGTAAT Chr17:64951112..64951131 60.38 50
upstream ENSMUSE00000306920 Chr17:64973868..64974119 CGCTGAGAACAACGAGATCA Chr17:64973918..64973937 60.14 50
upstream ENSMUSE00000306900 Chr17:64974647..64974791 ATCCAGATGGTGGAGTTTGG Chr17:64974681..64974700 59.78 50
upstream ENSMUSE00000495787 Chr17:64985824..64985995 CCTTGCAAAATGGTGGGATA Chr17:64985942..64985961 60.69 45

*** Putative Vector Insertion (Chr 17: 64985996 - 65000535) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000493264 Chr17:65000536..65000663 TGGCTTCATCAGGCATAACC Chr17:65000600..65000619 61 50
downstream ENSMUSE00000494670 Chr17:65008241..65008414 TGAAAATCCAGCACGCTTTA Chr17:65008329..65008348 59.44 40
downstream ENSMUSE00000491621 Chr17:65016077..65016263 TGTGAGGGATGTCGTAGCTG Chr17:65016145..65016164 59.85 55
downstream ENSMUSE00000138260 Chr17:65018752..65018929 CTGAACCGAAAGTCGTCTCC Chr17:65018847..65018866 59.84 55
downstream ENSMUSE00000138268 Chr17:65021188..65021390 GGTCTGGACGTGAAGTAGCC Chr17:65021351..65021370 59.73 60
downstream ENSMUSE00000138276 Chr17:65024405..65024587 GAGCTTGTTTCAAGGCCAAC Chr17:65024448..65024467 59.86 50
downstream ENSMUSE00000657073 Chr17:65029092..65029206 AAGGCTTTGGAAGGATCTGAC Chr17:65029198..65029218 59.71 47.62
downstream ENSMUSE00000657072 Chr17:65030895..65030965 CTCCTGTGCGCTCAGTTGTA Chr17:65030963..65030982 60.2 55
downstream ENSMUSE00000540937 Chr17:65060044..65060209 TTGTCCTCATGTCGTTCCAA Chr17:65060192..65060211 60.09 45
downstream ENSMUSE00000138264 Chr17:65061592..65061813 AGATCGGTCAAACCAAATCG Chr17:65061804..65061823 59.93 45
downstream ENSMUSE00000332597 Chr17:65062902..65063024 TGGACCTTCAGTTCATGCTG Chr17:65062951..65062970 59.83 50
downstream ENSMUSE00000450810 Chr17:65063938..65064052 AACGTGTTCGAGGAAACAGG Chr17:65064024..65064043 60.15 50
downstream ENSMUSE00000306603 Chr17:65080544..65080677 CTCACGGTTATGCACATTCC Chr17:65080611..65080630 59 50
downstream ENSMUSE00000138278 Chr17:65083064..65083205 AAGAGGCAATTTGCTCATGG Chr17:65083102..65083121 60.21 45
downstream ENSMUSE00000138275 Chr17:65084274..65084407 CGAGGAGGATTCGAAACAAA Chr17:65084387..65084406 60.18 45
downstream ENSMUSE00000138280 Chr17:65090020..65090223 TTGTATTGTCCGCAGGTTGA Chr17:65090220..65090239 60.11 45
downstream ENSMUSE00000414888 Chr17:65100124..65100234 CTCATCCGAATAGCCTTTGC Chr17:65100150..65100169 59.81 50
downstream ENSMUSE00000540934 Chr17:65101754..65104450 TTGAGGGATTGCACTTTTCC Chr17:65102424..65102443 60.05 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGTCGGATTGGATAAACGA Chr17:64997967..64997987 58.97 40 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGTATTTAAACCCGCGTGA Chr17:64998032..64998052 58.7 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024085