Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI37485
Trapped Gene
Ulk1 (ENSMUSG00000029512)
Vector Insertion
Chr 5: 111221415 - 111222133
Public Clones PST18943-NR (escells)
Private Clones not available
Severity of mutation (?) Insertion after 35% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000189720 (Chr5:111221985..111222132 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAGCAGCAAAGACTCCTGTG Chr5:111222024..111222043 59.77 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000189720 (Chr5:111221985..111222132 -)
Downstram Exon
ENSMUSE00000189719 (Chr5:111221416..111221476 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAGCAGCAAAGACTCCTGTG Chr5:111222024..111222043 59.77 55 ACACAGCAGGCTATCAGGTG Chr5:111221399..111221418 58.91 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000357368 Chr5:111238633..111239116 TGGGCAAGTTCGAGTTCTCT Chr5:111238693..111238712 59.99 50
upstream ENSMUSE00000189707 Chr5:111238146..111238238 CTTGCCAAGTCCCAAACACT Chr5:111238174..111238193 60.15 50
upstream ENSMUSE00000189694 Chr5:111238024..111238065 ATCGTGGCGCTGTATGACTT Chr5:111238028..111238047 60.69 50
upstream ENSMUSE00000189748 Chr5:111228143..111228175 No primer for this exon
upstream ENSMUSE00000406545 Chr5:111227901..111227937 ACCTGGCTGACTACCTGCAC Chr5:111227902..111227921 60.33 60
upstream ENSMUSE00000378719 Chr5:111225346..111225519 ATGCGCACACTGAGTGAAGA Chr5:111225498..111225517 60.63 50
upstream ENSMUSE00000189712 Chr5:111225175..111225248 GACTTTGGATTCGCTCGGTA Chr5:111225227..111225246 60.21 50
upstream ENSMUSE00000391857 Chr5:111224751..111224852 CTACGATGGAAAGGCTGACC Chr5:111224807..111224826 59.69 55
upstream ENSMUSE00000350353 Chr5:111223766..111223824 GGATTTGCGCCTGTTTTATG Chr5:111223791..111223810 60.46 45
upstream ENSMUSE00000189716 Chr5:111223604..111223686 No primer for this exon
upstream ENSMUSE00000189702 Chr5:111223212..111223262 GAATTTTTCCACCACCCTTTC Chr5:111223240..111223260 59.67 42.86
upstream ENSMUSE00000189708 Chr5:111222834..111222922 GTGCCCTCATATCCAAGCTC Chr5:111222889..111222908 59.66 55
upstream ENSMUSE00000189720 Chr5:111221985..111222132 CAGCAGCAAAGACTCCTGTG Chr5:111222024..111222043 59.77 55
upstream ENSMUSE00000189719 Chr5:111221416..111221476 CACCTGATAGCCTGCTGTGT Chr5:111221421..111221440 58.91 55

*** Putative Vector Insertion (Chr 5: 111221415 - 111222133) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000189714 Chr5:111221121..111221210 No primer for this exon
downstream ENSMUSE00000189718 Chr5:111220620..111220745 GCTGGTAATTGTGCACCTGA Chr5:111220644..111220663 59.72 50
downstream ENSMUSE00000189731 Chr5:111220071..111220216 TTGGGGAGAAGGTGTGTAGG Chr5:111220050..111220069 59.96 55
downstream ENSMUSE00000189744 Chr5:111219869..111219955 No primer for this exon
downstream ENSMUSE00000691628 Chr5:111219869..111219973 No primer for this exon
downstream ENSMUSE00000189717 Chr5:111219231..111219499 TGGAAGTCGGACAGGTTAGG Chr5:111219396..111219415 60.1 55
downstream ENSMUSE00000189729 Chr5:111218361..111218554 GGTCAGGCAGTGTACGGTTC Chr5:111218421..111218440 60.58 60
downstream ENSMUSE00000189695 Chr5:111217967..111218076 GAGTCCCAAATGCAGCCTTA Chr5:111217999..111218018 60.21 50
downstream ENSMUSE00000189705 Chr5:111217748..111217891 GATGCAGAGTCCCTCCAAAG Chr5:111217837..111217856 59.8 55
downstream ENSMUSE00000189741 Chr5:111217129..111217319 GGTCAGCAAGGCTACAGCAG Chr5:111217178..111217197 61.14 60
downstream ENSMUSE00000189691 Chr5:111216792..111216964 GTGTAGGGTTTCCGTGTGCT Chr5:111216919..111216938 60.03 55
downstream ENSMUSE00000189724 Chr5:111216593..111216711 CCAGCTCGAATCTGGTCAAT Chr5:111216603..111216622 60.22 50
downstream ENSMUSE00000189700 Chr5:111216103..111216260 CCAGAAAGAAGCGCTGAAGT Chr5:111216155..111216174 59.76 50
downstream ENSMUSE00000189698 Chr5:111215319..111215454 CAGCAATAGCAGGGCTTTGT Chr5:111215352..111215371 60.41 50
downstream ENSMUSE00000295761 Chr5:111213507..111215246 TGCTGGCTAGGTTCTCCAGT Chr5:111214645..111214664 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTACAGTCCCTGGGGGAGAT Chr5:111222117..111222137 60.33 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTACAGTCCCTGGGGGAGAT Chr5:111222117..111222137 60.33 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029512