Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9669
Trapped Gene
Manba (ENSMUSG00000028164)
Vector Insertion
Chr 3: 135212332 - 135214026
Public Clones (sanger) Ex158 (baygenomics) XG655 (baygenomics) XG461 (baygenomics)
E041A05 (ggtc) P009E10 (ggtc) CMHD-GT_469C11-3 (cmhd) IST14652C12 (tigm)
IST11142A8 (tigm) IST14731A11 (tigm) IST14814E5 (tigm)
Private Clones OST206583 (lexicon) OST36805 (lexicon)
Severity of mutation (?) Insertion after 56% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000176940 (Chr3:135212164..135212331 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGTGGCTCTCAGCGTGAACT Chr3:135212223..135212242 60.21 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000176940 (Chr3:135212164..135212331 +)
Downstram Exon
ENSMUSE00000500705 (Chr3:135214027..135214245 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGTGGCTCTCAGCGTGAACT Chr3:135212223..135212242 60.21 55 TGAAAGGACGGCTCTTGTCT Chr3:135214051..135214070 59.99 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000242269 Chr3:135148578..135148821 AGCATGCATCTTCACCTGCT Chr3:135148642..135148661 60.98 50
upstream ENSMUSE00000242259 Chr3:135169873..135169967 GGACCTACAGCACGGAATTT Chr3:135169928..135169947 59.06 50
upstream ENSMUSE00000242249 Chr3:135173939..135174044 GACACGGTTGCAGAAATCCT Chr3:135173976..135173995 60.12 50
upstream ENSMUSE00000242240 Chr3:135174767..135174937 CACGTCAACTTCATCCGAAA Chr3:135174917..135174936 59.69 45
upstream ENSMUSE00000242234 Chr3:135180867..135180990 TGGATTACCTCACGTTTTTGC Chr3:135180961..135180981 59.99 42.86
upstream ENSMUSE00000242226 Chr3:135185956..135186131 AGCTCGAAGTCCGTTAGTGG Chr3:135186009..135186028 59.5 55
upstream ENSMUSE00000176937 Chr3:135187481..135187591 GGGAACCAGACTGGGTACAA Chr3:135187517..135187536 59.82 55
upstream ENSMUSE00000176926 Chr3:135205276..135205427 GAGGGCATAAAAGGGTCTCC Chr3:135205306..135205325 59.9 55
upstream ENSMUSE00000176931 Chr3:135207690..135207807 GTGGCATCTACGAGCAGGAT Chr3:135207752..135207771 60.25 55
upstream ENSMUSE00000446365 Chr3:135210514..135210600 TAGCCTCCGTGAGGAAAGAA Chr3:135210569..135210588 59.95 50
upstream ENSMUSE00000176940 Chr3:135212164..135212331 AGTGGCTCTCAGCGTGAACT Chr3:135212223..135212242 60.21 55

*** Putative Vector Insertion (Chr 3: 135212332 - 135214026) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000500705 Chr3:135214027..135214245 TGAAAGGACGGCTCTTGTCT Chr3:135214051..135214070 59.99 50
downstream ENSMUSE00000176942 Chr3:135217724..135217888 GGAGAAGCGGCTGTTGTAAG Chr3:135217768..135217787 60.01 55
downstream ENSMUSE00000414334 Chr3:135226169..135226313 GGCCTTTTCCGTCCACTATC Chr3:135226250..135226269 60.83 55
downstream ENSMUSE00000445781 Chr3:135229452..135229594 AACAGTGGAGCGAAGAAACG Chr3:135229515..135229534 60.43 50
downstream ENSMUSE00000242177 Chr3:135230428..135230685 CTCCGGCCTTAACCACAATA Chr3:135230506..135230525 59.95 50
downstream ENSMUSE00000414715 Chr3:135233179..135234293 AGTCTTCTGGCCGTGCTTTA Chr3:135233641..135233660 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AATGGTTTGGGGCAGTAGAA Chr3:135212339..135212359 59.43 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AATGGTTTGGGGCAGTAGAA Chr3:135212339..135212359 59.43 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028164