Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI19389
Trapped Gene
Arhgap17 (ENSMUSG00000030766)
Vector Insertion
Chr 7: 130423631 - 130428933
Public Clones IST10641D8 (tigm)
Private Clones OST392437 (lexicon)
Severity of mutation (?) Insertion after 95% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000669938 (Chr7:130428934..130428981 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTCACAGGTGGGGAAGGTTT Chr7:130428945..130428964 61.31 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000669938 (Chr7:130428934..130428981 -)
Downstram Exon
ENSMUSE00000669936 (Chr7:130422789..130423630 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTCACAGGTGGGGAAGGTTT Chr7:130428945..130428964 61.31 55 TTGCTTGCCAAGTCTGAATG Chr7:130423539..130423558 59.99 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000669939 Chr7:130513268..130513392 GTAGGTAGGACCCGCCAGAC Chr7:130513373..130513392 60.9 65
upstream ENSMUSE00000669962 Chr7:130513268..130513405 GTAGGTAGGACCCGCCAGAC Chr7:130513373..130513392 60.9 65
upstream ENSMUSE00000632588 Chr7:130474740..130474779 AGCTGAGAAGACCGAAGTCC Chr7:130474760..130474779 58.62 55
upstream ENSMUSE00000632587 Chr7:130470753..130470857 CTGGACACTGTGCGTTCAAT Chr7:130470826..130470845 59.75 50
upstream ENSMUSE00000632586 Chr7:130467127..130467200 AGAACATGCAGGAGGCTTCA Chr7:130467153..130467172 60.94 50
upstream ENSMUSE00000632585 Chr7:130465393..130465504 TGGACCCTCTCTACGGCATA Chr7:130465399..130465418 60.62 55
upstream ENSMUSE00000632584 Chr7:130465102..130465178 GGTGTTGGACTGGGATTCAG Chr7:130465112..130465131 60.36 55
upstream ENSMUSE00000632583 Chr7:130461901..130462012 AGGGGCTTCCATCCAAAATA Chr7:130461955..130461974 60.63 45
upstream ENSMUSE00000632582 Chr7:130458158..130458226 GCCAAAGAAGGGGAGTATGG Chr7:130458174..130458193 60.82 55
upstream ENSMUSE00000632580 Chr7:130457928..130458009 GAAGCCCAAGCAGATTACCA Chr7:130457984..130458003 60.21 50
upstream ENSMUSE00000632579 Chr7:130451800..130451927 GGAGACTGGCATGAAAGAGG Chr7:130451802..130451821 59.8 55
upstream ENSMUSE00000632578 Chr7:130450482..130450593 AAAGCTGCTCTCGACTGCTC Chr7:130450529..130450548 60.04 55
upstream ENSMUSE00000632577 Chr7:130449889..130449970 AGTCCTATCTGCGGGAGTTG Chr7:130449942..130449961 59.31 55
upstream ENSMUSE00000632576 Chr7:130447210..130447290 AGAAGTTGCCGCCACAAAAT Chr7:130447224..130447243 61.91 45
upstream ENSMUSE00000632575 Chr7:130444003..130444116 GCAACATAGCCATTGTCCTG Chr7:130444035..130444054 59.15 50
upstream ENSMUSE00000632574 Chr7:130441009..130441100 AGTGATTGAGCCCATCATCC Chr7:130441036..130441055 59.89 50
upstream ENSMUSE00000632573 Chr7:130439924..130440080 TGACTCTGACTCGGGGACTC Chr7:130439985..130440004 60.4 60
upstream ENSMUSE00000202967 Chr7:130437986..130438219 CTACGGGCATATTGGAGCAG Chr7:130438009..130438028 60.62 55
upstream ENSMUSE00000632572 Chr7:130435550..130435719 GAACAGCAACCAGATGACCA Chr7:130435649..130435668 59.68 50
upstream ENSMUSE00000632592 Chr7:130430130..130430527 ATCCATCGCAAAGTGAGACC Chr7:130430163..130430182 60.08 50
upstream ENSMUSE00000632591 Chr7:130430096..130430128 No primer for this exon
upstream ENSMUSE00000632590 Chr7:130430013..130430093 ATGGTGGCCTTACATCCTCA Chr7:130430040..130430059 60.34 50
upstream ENSMUSE00000632571 Chr7:130430012..130430527 ATCCATCGCAAAGTGAGACC Chr7:130430163..130430182 60.08 50
upstream ENSMUSE00000669935 Chr7:130429816..130429820 No primer for this exon
upstream ENSMUSE00000669938 Chr7:130428934..130428981 CTCACAGGTGGGGAAGGTTT Chr7:130428945..130428964 61.31 55

*** Putative Vector Insertion (Chr 7: 130423631 - 130428933) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000669936 Chr7:130422789..130423630 TTGCTTGCCAAGTCTGAATG Chr7:130423539..130423558 59.99 45
downstream ENSMUSE00000632570 Chr7:130422785..130423630 TTGCTTGCCAAGTCTGAATG Chr7:130423539..130423558 59.99 45
downstream ENSMUSE00000669940 Chr7:130350805..130350818 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTCACAGGTGGGGAAGGTTT Chr7:130428943..130428963 61.31 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTAGCCGTGACTGGGAAAAC Chr7:130428867..130428887 60.11 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCAGGTCCATCTCACTGTCC Chr7:130428956..130428976 60.53 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCAGGTCCATCTCACTGTCC Chr7:130428956..130428976 60.53 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030766