Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI15514
Trapped Gene
Dnajb6 (ENSMUSG00000029131)
Vector Insertion
Chr 5: 30079000 - 30080081
Public Clones PST8780-NR (escells)
Private Clones OST251387 (lexicon) OST88518 (lexicon)
Severity of mutation (?) Insertion after 31% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000185979 (Chr5:30078937..30078999 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCGGGACATCTACGACAAAT Chr5:30078944..30078963 59.96 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000185979 (Chr5:30078937..30078999 +)
Downstram Exon
ENSMUSE00000185975 (Chr5:30080082..30080192 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCGGGACATCTACGACAAAT Chr5:30078944..30078963 59.96 50 CGGAATGTGAAGCCAAACTC Chr5:30080130..30080149 60.64 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000700760 Chr5:30062480..30062656 TGACGCACTTCCTGTTTGTT Chr5:30062508..30062527 59.34 45
upstream ENSMUSE00000185970 Chr5:30062568..30062656 No primer for this exon
upstream ENSMUSE00000185974 Chr5:30074885..30074975 TGCCTCACCTGAGGACATTA Chr5:30074949..30074968 59.24 50
upstream ENSMUSE00000710480 Chr5:30074885..30074975 TGCCTCACCTGAGGACATTA Chr5:30074949..30074968 59.24 50
upstream ENSMUSE00000185969 Chr5:30077478..30077587 AAGCAGAGCGGAAGTTCAAA Chr5:30077534..30077553 60.13 45
upstream ENSMUSE00000185979 Chr5:30078937..30078999 GCGGGACATCTACGACAAAT Chr5:30078944..30078963 59.96 50

*** Putative Vector Insertion (Chr 5: 30079000 - 30080081) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000185975 Chr5:30080082..30080192 CGGAATGTGAAGCCAAACTC Chr5:30080130..30080149 60.64 50
downstream ENSMUSE00000185978 Chr5:30082774..30082878 TGCACGGTCACCTCATACAC Chr5:30082870..30082889 60.6 55
downstream ENSMUSE00000185980 Chr5:30084088..30084419 CCTCACTGTGCTCGTCACTC Chr5:30084195..30084214 59.6 60
downstream ENSMUSE00000185972 Chr5:30090939..30091070 GCAGGAAATCCACTTCCAAA Chr5:30091062..30091081 60.05 45
downstream ENSMUSE00000185973 Chr5:30092046..30092187 ATTTGAAGTTGCCCATTCCA Chr5:30092138..30092157 60.31 40
downstream ENSMUSE00000655112 Chr5:30092865..30092935 TTTCTTGACCGTTCTCCACA Chr5:30092890..30092909 59.26 45
downstream ENSMUSE00000700759 Chr5:30092865..30093643 GCGTAGCAGGTGCTCCTTAC Chr5:30092958..30092977 60.04 60
downstream ENSMUSE00000655109 Chr5:30107670..30107990 CCTGTCCTGCTCGTCATCTT Chr5:30107950..30107969 60.41 55
downstream ENSMUSE00000655108 Chr5:30111571..30111653 TCCTCTTGCCACCTTCTTTG Chr5:30111597..30111616 60.37 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGTGGTGGAGGAGGAGGTAT Chr5:30078985..30079005 60.19 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTGGTGGAGGAGGAGGTAT Chr5:30078985..30079005 60.19 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029131