Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9509
Trapped Gene
Usp6nl (ENSMUSG00000039046)
Vector Insertion
Chr 2: 6351625 - 6361406
Public Clones RRA055 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 46% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000311752 (Chr2:6351472..6351624 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAGAACTAAAGCGGGCAAAG Chr2:6351586..6351605 60.01 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000311752 (Chr2:6351472..6351624 +)
Downstram Exon
ENSMUSE00000570152 (Chr2:6361407..6364866 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAGAACTAAAGCGGGCAAAG Chr2:6351586..6351605 60.01 50 AAGGTGATGCGGTTCAAAAC Chr2:6364705..6364724 59.98 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000701187 Chr2:6243713..6244000 CCTCCTGGAAGGGAAACAAT Chr2:6243884..6243903 60.3 50
upstream ENSMUSE00000701195 Chr2:6243803..6244000 CCTCCTGGAAGGGAAACAAT Chr2:6243884..6243903 60.3 50
upstream ENSMUSE00000605430 Chr2:6257414..6257505 ACCCACAGAGGTTTGCAGTC Chr2:6257482..6257501 60.16 55
upstream ENSMUSE00000712373 Chr2:6257414..6257505 ACCCACAGAGGTTTGCAGTC Chr2:6257482..6257501 60.16 55
upstream ENSMUSE00000430099 Chr2:6273782..6273910 No primer for this exon
upstream ENSMUSE00000311852 Chr2:6312101..6312168 TGCTCAAGAACGAGCTGAAA Chr2:6312129..6312148 59.86 45
upstream ENSMUSE00000311845 Chr2:6315519..6315601 TCACCGATAGATTTGGCTTTTT Chr2:6315577..6315598 59.97 36.36
upstream ENSMUSE00000311835 Chr2:6321326..6321365 AGGAGGAGCTCCCATACCAT Chr2:6321328..6321347 59.92 55
upstream ENSMUSE00000311826 Chr2:6329975..6330055 GCAACTGGAAATCGAAAGGA Chr2:6329980..6329999 60.19 45
upstream ENSMUSE00000311818 Chr2:6335979..6336086 CAGCTCCGAGGTGAAGTCTG Chr2:6336012..6336031 61.14 60
upstream ENSMUSE00000311807 Chr2:6341949..6342058 ACGGGGTTGTTCACCTGATA Chr2:6341966..6341985 60.23 50
upstream ENSMUSE00000311797 Chr2:6344468..6344516 TTCCATGTTCTCGCTGCTTA Chr2:6344481..6344500 59.57 45
upstream ENSMUSE00000311789 Chr2:6345318..6345438 ACTGCCAAGGGATGAGTCAG Chr2:6345328..6345347 60.26 55
upstream ENSMUSE00000311781 Chr2:6347941..6348035 No primer for this exon
upstream ENSMUSE00000311769 Chr2:6348598..6348663 No primer for this exon
upstream ENSMUSE00000311761 Chr2:6348758..6348857 GGAGAGCGAGTCCTTACTGC Chr2:6348806..6348825 59.19 60
upstream ENSMUSE00000311752 Chr2:6351472..6351624 CAGAACTAAAGCGGGCAAAG Chr2:6351586..6351605 60.01 50

*** Putative Vector Insertion (Chr 2: 6351625 - 6361406) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000430092 Chr2:6361407..6367436 AAGACCGAGTGCCAGAGAAA Chr2:6363655..6363674 59.99 50
downstream ENSMUSE00000570152 Chr2:6361407..6364866 AAGGTGATGCGGTTCAAAAC Chr2:6364705..6364724 59.98 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGACAAGATAATCGCCTTGC Chr2:6351668..6351688 59.67 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCTGGTAAGAAGTGCCTTG Chr2:6351621..6351641 59.88 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039046