Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5069
Trapped Gene
Dlg1 (ENSMUSG00000022770)
Vector Insertion
Chr 16: 31829655 - 31836275
Public Clones YTC550 (baygenomics) A071B04 (ggtc)
Private Clones OST34365 (lexicon)
Severity of mutation (?) Insertion after 55% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000230810 (Chr16:31829552..31829654 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAGCTGCAAGTCACGAACAA Chr16:31829571..31829590 60.18 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000230810 (Chr16:31829552..31829654 +)
Downstram Exon
ENSMUSE00000230805 (Chr16:31836276..31836390 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAGCTGCAAGTCACGAACAA Chr16:31829571..31829590 60.18 50 TGGTTCGAAGAGACCCTGAC Chr16:31836368..31836387 60.24 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000434992 Chr16:31663529..31663574 GTGAGGGGTGTCTTGAGCTT Chr16:31663534..31663553 59.31 55
upstream ENSMUSE00000644422 Chr16:31663995..31664407 No primer for this exon
upstream ENSMUSE00000434707 Chr16:31664125..31664407 No primer for this exon
upstream ENSMUSE00000702035 Chr16:31664236..31664407 No primer for this exon
upstream ENSMUSE00000334814 Chr16:31664907..31664956 No primer for this exon
upstream ENSMUSE00000709094 Chr16:31664907..31664956 No primer for this exon
upstream ENSMUSE00000375424 Chr16:31665661..31665792 AGAGCATTGCATCTGTTGGA Chr16:31665669..31665688 59.4 45
upstream ENSMUSE00000230857 Chr16:31684214..31684380 GTGAACCAGTTCAGCCTGTG Chr16:31684280..31684299 59.31 55
upstream ENSMUSE00000130290 Chr16:31743192..31743356 CCGGTATCAGGATGAAGAGGT Chr16:31743197..31743217 60.33 52.38
upstream ENSMUSE00000702027 Chr16:31754436..31755102 AAGGGTCTTGGTAGCCCAGT Chr16:31754461..31754480 59.99 55
upstream ENSMUSE00000130294 Chr16:31771843..31771941 GCCAGTCCCTGCTGAGAGTA Chr16:31771896..31771915 60.56 60
upstream ENSMUSE00000702029 Chr16:31771843..31772010 GCCAGTCCCTGCTGAGAGTA Chr16:31771896..31771915 60.56 60
upstream ENSMUSE00000130301 Chr16:31781868..31781921 TGCTGGTCAACACAGACAGC Chr16:31781884..31781903 61.1 55
upstream ENSMUSE00000130286 Chr16:31788168..31788218 TGGCACTGATGCAGATTATGA Chr16:31788173..31788193 60.24 42.86
upstream ENSMUSE00000130284 Chr16:31790263..31790387 GGAAATTCGGGTCTTGGTTT Chr16:31790263..31790282 60.17 45
upstream ENSMUSE00000130288 Chr16:31791801..31791970 GTATGTGAAAAGGCGGAAGC Chr16:31791903..31791922 59.71 50
upstream ENSMUSE00000130298 Chr16:31793590..31793726 GGCAAGCTTCAGATTGGAGA Chr16:31793694..31793713 60.48 50
upstream ENSMUSE00000130296 Chr16:31796952..31797096 GCTATGCACCACCTGACATC Chr16:31797070..31797089 59.12 55
upstream ENSMUSE00000130283 Chr16:31805700..31805820 GTGCTCGGAGATGACGAGAT Chr16:31805795..31805814 60.38 55
upstream ENSMUSE00000230817 Chr16:31812754..31812910 TCTTCATCGTGGCTCAACAG Chr16:31812772..31812791 59.98 50
upstream ENSMUSE00000230810 Chr16:31829552..31829654 GAGCTGCAAGTCACGAACAA Chr16:31829571..31829590 60.18 50

*** Putative Vector Insertion (Chr 16: 31829655 - 31836275) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000230805 Chr16:31836276..31836390 TGGTTCGAAGAGACCCTGAC Chr16:31836368..31836387 60.24 55
downstream ENSMUSE00000230798 Chr16:31838136..31838312 CTCCGACTTCGTCACTCTCC Chr16:31838296..31838315 59.99 60
downstream ENSMUSE00000230790 Chr16:31842856..31842925 TTTTAATCGGGCTCGTTCCT Chr16:31842889..31842908 60.92 45
downstream ENSMUSE00000511839 Chr16:31846920..31847019 CAGCATCACTCGTTTCCTGT Chr16:31847019..31847038 58.88 50
downstream ENSMUSE00000702050 Chr16:31846923..31847019 TCAGCATCACTCGTTTCCTG Chr16:31847020..31847039 59.98 50
downstream ENSMUSE00000434693 Chr16:31847722..31847755 CCTTTTGATCCCATGTCGTC Chr16:31847753..31847772 60.32 50
downstream ENSMUSE00000230778 Chr16:31853929..31853970 CGCTGGCATTAGAAGTTACG Chr16:31853955..31853974 58.61 50
downstream ENSMUSE00000702026 Chr16:31854739..31854774 CTTTTGAGCAGCCATATTCATC Chr16:31854775..31854796 58.86 40.91
downstream ENSMUSE00000702039 Chr16:31854754..31854774 No primer for this exon
downstream ENSMUSE00000230770 Chr16:31856527..31856577 No primer for this exon
downstream ENSMUSE00000521165 Chr16:31857633..31857734 CAGGATCCAAATTTGTCAGGA Chr16:31857728..31857748 59.92 42.86
downstream ENSMUSE00000559866 Chr16:31857978..31858150 GCTCGTCCCATACAGATGGT Chr16:31858123..31858142 59.96 55
downstream ENSMUSE00000230750 Chr16:31863259..31863368 TGTGCAATCTGCAACCTCTT Chr16:31863320..31863339 59.44 45
downstream ENSMUSE00000230745 Chr16:31867917..31868008 TGTTTTTCTGGCCTGCTCTT Chr16:31867962..31867981 59.99 45
downstream ENSMUSE00000434713 Chr16:31871761..31872347 CTGGTCAGGCCATTCATCTT Chr16:31872090..31872109 60.07 50
downstream ENSMUSE00000702033 Chr16:31871761..31872770 GGGAGGGCACACAATAAAGA Chr16:31872459..31872478 59.93 50
downstream ENSMUSE00000702038 Chr16:31871761..31871932 AAATGTCCTCCAGCGTGTCT Chr16:31871796..31871815 59.73 50
downstream ENSMUSE00000702048 Chr16:31871761..31873436 TGCCAAAATCACGTATCGAA Chr16:31873339..31873358 60.07 40
downstream ENSMUSE00000702054 Chr16:31871761..31873428 TGCCAAAATCACGTATCGAA Chr16:31873339..31873358 60.07 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CGAAGGTGAGACGGTTTTGT Chr16:31835651..31835671 60.15 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGAAGGTGAGACGGTTTTGT Chr16:31835651..31835671 60.15 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000022770