Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI37991
Trapped Gene
Ntrk2 (ENSMUSG00000055254)
Vector Insertion
Chr 13: 59087352 - 59139327
Public Clones (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 61% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000452376 (Chr13:59087163..59087351 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTCCCGACGCTGTCATTATT Chr13:59087256..59087275 59.96 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000452376 (Chr13:59087163..59087351 +)
Downstram Exon
ENSMUSE00000452370 (Chr13:59139328..59139458 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTCCCGACGCTGTCATTATT Chr13:59087256..59087275 59.96 50 GGGCAGAGGTTGTAGCACTC Chr13:59139430..59139449 59.87 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000453182 Chr13:58909261..58909374 ACTGTCCTGCTACCGCAGTT Chr13:58909346..58909365 59.94 55
upstream ENSMUSE00000482157 Chr13:58909746..58910301 CGAGGTTGGAACCTAACAGC Chr13:58910256..58910275 59.73 55
upstream ENSMUSE00000453197 Chr13:58939157..58939231 CTTACGTGGGGCTGAGAAAC Chr13:58939210..58939229 59.73 55
upstream ENSMUSE00000453177 Chr13:58939346..58939417 TTCCGGCTTAAAGTTTGTGG Chr13:58939358..58939377 60.1 45
upstream ENSMUSE00000453172 Chr13:58944237..58944305 CAAGCTGACGAGTTTGTCCA Chr13:58944252..58944271 60.03 50
upstream ENSMUSE00000453169 Chr13:58948061..58948215 CGAACCTGCAGATACCCAAT Chr13:58948192..58948211 59.96 50
upstream ENSMUSE00000452404 Chr13:58960530..58960666 ACCTTGTACTGGGACGTTGG Chr13:58960625..58960644 59.88 55
upstream ENSMUSE00000452401 Chr13:58961507..58961639 TTGTGTGGCAGAAAACCTTG Chr13:58961581..58961600 59.73 45
upstream ENSMUSE00000452398 Chr13:58962611..58962916 ATGGCCAAGAACGAGTATGG Chr13:58962841..58962860 59.96 50
upstream ENSMUSE00000452394 Chr13:58973097..58973132 CCCAAATTACCCTGAAGTCC Chr13:58973104..58973123 58.36 50
upstream ENSMUSE00000681770 Chr13:58973097..58973131 CCCAAATTACCCTGAAGTCC Chr13:58973104..58973123 58.36 50
upstream ENSMUSE00000681768 Chr13:58975688..58975786 GCCAACTGACATTGGGGATA Chr13:58975699..58975718 60.72 50
upstream ENSMUSE00000452388 Chr13:58975689..58975786 GCCAACTGACATTGGGGATA Chr13:58975699..58975718 60.72 50
upstream ENSMUSE00000452382 Chr13:58979524..58979623 AGTTGGCGAGACATTCCAAG Chr13:58979591..58979610 60.26 50
upstream ENSMUSE00000681760 Chr13:59033384..59033421 AAGATCCCACTGGATGGGTA Chr13:59033401..59033420 59.21 50
upstream ENSMUSE00000452376 Chr13:59087163..59087351 GTCCCGACGCTGTCATTATT Chr13:59087256..59087275 59.96 50

*** Putative Vector Insertion (Chr 13: 59087352 - 59139327) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000452370 Chr13:59139328..59139458 GGGCAGAGGTTGTAGCACTC Chr13:59139430..59139449 59.87 60
downstream ENSMUSE00000183030 Chr13:59155654..59155826 AGCTTCCCGATGAAAGTCCT Chr13:59155707..59155726 60.21 50
downstream ENSMUSE00000452359 Chr13:59161589..59161823 GCTGTACACATCTCGGGACA Chr13:59161811..59161830 59.71 55
downstream ENSMUSE00000614570 Chr13:59227794..59227952 TGCTTGCCGTAGGTGAAGAT Chr13:59227927..59227946 60.8 50
downstream ENSMUSE00000453213 Chr13:59229529..59235331 AAAGAAGTGAAGGGCTGCAA Chr13:59234305..59234324 59.99 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTTGCATCCCCTATAATCG Chr13:59096389..59096409 59.53 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGGACCTGTTGTGAAATGGT Chr13:59096347..59096367 59.68 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000055254