Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7878
Trapped Gene
Manba (ENSMUSG00000028164)
Vector Insertion
Chr 3: 135148822 - 135169872
Public Clones RRJ641 (baygenomics) M117C06 (ggtc) D168G02 (ggtc) P075A12 (ggtc)
D168G02 (ggtc) G014D03 (ggtc) IST11302F8 (tigm) IST10935B11 (tigm)
IST11060F7 (tigm) IST10067A4 (tigm) IST12824H11 (tigm) IST12764B10 (tigm)
IST11816H11 (tigm) IST14789A9 (tigm) IST12506B7 (tigm) IST13087H10 (tigm)
IST10439B5 (tigm) IST14780D4 (tigm) IST11816H11 (tigm) IST12651G9 (tigm)
IST10657E9 (tigm) IST12239A12 (tigm) IST10083F10 (tigm) IST11939A10 (tigm)
IST11060F7 (tigm) IST12048A2 (tigm) IST14852E7 (tigm) IST12506B7 (tigm)
IST11491H5 (tigm) IST14914F11 (tigm) IST10084A1 (tigm) IST12754A12 (tigm)
IST10657E9 (tigm) IST14870A2 (tigm)
Private Clones OST214346 (lexicon)
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000242269 (Chr3:135148578..135148821 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCATGCATCTTCACCTGCT Chr3:135148642..135148661 60.98 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000242269 (Chr3:135148578..135148821 +)
Downstram Exon
ENSMUSE00000242259 (Chr3:135169873..135169967 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCATGCATCTTCACCTGCT Chr3:135148642..135148661 60.98 50 AATTCCGTGCTGTAGGTCCA Chr3:135169949..135169968 60.52 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

*** Putative Vector Insertion (Chr 3: 135148822 - 135169872) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000242259 Chr3:135169873..135169967 AATTCCGTGCTGTAGGTCCA Chr3:135169949..135169968 60.52 50
downstream ENSMUSE00000242249 Chr3:135173939..135174044 AGGATTTCTGCAACCGTGTC Chr3:135173998..135174017 60.12 50
downstream ENSMUSE00000242240 Chr3:135174767..135174937 GTGTGAGCCTTGCTCTGACA Chr3:135174867..135174886 60.19 55
downstream ENSMUSE00000242234 Chr3:135180867..135180990 AGATTCCCTGAGAGGGGAAG Chr3:135180924..135180943 59.63 55
downstream ENSMUSE00000242226 Chr3:135185956..135186131 TTGAGGGATGGCTACTGTCA Chr3:135186056..135186075 59.24 50
downstream ENSMUSE00000176937 Chr3:135187481..135187591 CCTCCATCCAGAGCAAAGAG Chr3:135187569..135187588 59.94 55
downstream ENSMUSE00000176926 Chr3:135205276..135205427 AGTCGGCTGGAATCCAATTT Chr3:135205402..135205421 60.83 45
downstream ENSMUSE00000176931 Chr3:135207690..135207807 GAGTGTTCATGTTCGCATCC Chr3:135207739..135207758 59.09 50
downstream ENSMUSE00000446365 Chr3:135210514..135210600 TTTCCTCACGGAGGCTAAGA Chr3:135210588..135210607 59.95 50
downstream ENSMUSE00000176940 Chr3:135212164..135212331 ATGTCCCTGGGATTTACGTG Chr3:135212270..135212289 59.67 50
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 ATCCAGGTAGGACGCACAGT Chr3:135148817..135148837 59.6 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAACACGTGACTGGGAAAAC Chr3:135151868..135151888 59.03 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028164