Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI141
Trapped Gene
Dnajb6 (ENSMUSG00000029131)
Vector Insertion
Chr 5: 30092864 - 30092936
Public Clones GC0563 (tigem) GC0567 (tigem) GC0116 (tigem) CSH473 (baygenomics) XG040 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000655112 (Chr5:30092865..30092935 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTGGAGAACGGTCAAGAAA Chr5:30092868..30092887 59.26 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000655112 (Chr5:30092865..30092935 +)
Downstram Exon
ENSMUSE00000700759 (Chr5:30092865..30093643 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTGGAGAACGGTCAAGAAA Chr5:30092868..30092887 59.26 45 GCGTAGCAGGTGCTCCTTAC Chr5:30092958..30092977 60.04 60

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
upstream ENSMUSE00000185975 Chr5:30080082..30080192 CGGAACCCAGATGATGTCTT Chr5:30080126..30080145 59.93 50
upstream ENSMUSE00000185978 Chr5:30082774..30082878 GGATTTTCGCACAGGAAAAG Chr5:30082807..30082826 59.69 45
upstream ENSMUSE00000185980 Chr5:30084088..30084419 GCTCAGCGAGGAGTATGAGG Chr5:30084338..30084357 60.12 60
upstream ENSMUSE00000185972 Chr5:30090939..30091070 GGTCCCCGAGGAAATAGAAG Chr5:30090974..30090993 59.9 55
upstream ENSMUSE00000185973 Chr5:30092046..30092187 CATGGGGGTCTCACTTCATT Chr5:30092072..30092091 59.78 50

*** Putative Vector Insertion (Chr 5: 30092864 - 30092936) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TCCCGATTGAACAGAGGTTT Chr5:30092824..30092844 59.53 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCCCGATTGAACAGAGGTTT Chr5:30092824..30092844 59.53 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029131