Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5916
Trapped Gene
Dip2c (ENSMUSG00000048264)
Vector Insertion
Chr 13: 9505824 - 9505936
Public Clones CSH142 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000684778 (Chr13:9505825..9505935 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCTCAGGGTCTCGAGATGAA Chr13:9505903..9505922 60.34 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000684778 (Chr13:9505825..9505935 +)
Downstram Exon
ENSMUSE00000452316 (Chr13:9505825..9505935 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCTCAGGGTCTCGAGATGAA Chr13:9505903..9505922 60.34 55 CATCTCGAGACCCTGAGGAC Chr13:9505923..9505942 59.79 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000684802 Chr13:9276228..9276312 No primer for this exon
upstream ENSMUSE00000482344 Chr13:9492349..9492422 No primer for this exon
upstream ENSMUSE00000684801 Chr13:9492351..9492422 No primer for this exon

*** Putative Vector Insertion (Chr 13: 9505824 - 9505936) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000452316 Chr13:9505825..9505935 CATCTCGAGACCCTGAGGAC Chr13:9505923..9505942 59.79 60
downstream ENSMUSE00000684778 Chr13:9505825..9505935 CATCTCGAGACCCTGAGGAC Chr13:9505923..9505942 59.79 60
downstream ENSMUSE00000115147 Chr13:9532498..9532623 CAGGGATCTTCGTTTGGAAG Chr13:9532589..9532608 59.67 50
downstream ENSMUSE00000684777 Chr13:9532498..9532623 CAGGGATCTTCGTTTGGAAG Chr13:9532589..9532608 59.67 50
downstream ENSMUSE00000115125 Chr13:9535902..9536111 TGATCCAATGCTCCATGTTG Chr13:9536003..9536022 60.48 45
downstream ENSMUSE00000684776 Chr13:9535902..9536111 TGATCCAATGCTCCATGTTG Chr13:9536003..9536022 60.48 45
downstream ENSMUSE00000251820 Chr13:9549430..9549564 TGCCATACTTTGGTGCTGTC Chr13:9549540..9549559 59.72 50
downstream ENSMUSE00000684774 Chr13:9549430..9549564 TGCCATACTTTGGTGCTGTC Chr13:9549540..9549559 59.72 50
downstream ENSMUSE00000643937 Chr13:9550992..9551111 GCTTCGGTCGTTTAAGGGTA Chr13:9551063..9551082 59.22 50
downstream ENSMUSE00000684798 Chr13:9550992..9551111 GCTTCGGTCGTTTAAGGGTA Chr13:9551063..9551082 59.22 50
downstream ENSMUSE00000684773 Chr13:9552520..9552717 TAAAGAGGGTGGCCAGTTTG Chr13:9552623..9552642 60.1 50
downstream ENSMUSE00000684797 Chr13:9552520..9552717 TAAAGAGGGTGGCCAGTTTG Chr13:9552623..9552642 60.1 50
downstream ENSMUSE00000684772 Chr13:9559917..9560008 GTCTCCAGGCCGTACCATAG Chr13:9560008..9560027 59.57 60
downstream ENSMUSE00000684795 Chr13:9559917..9560008 GTCTCCAGGCCGTACCATAG Chr13:9560008..9560027 59.57 60
downstream ENSMUSE00000115140 Chr13:9562360..9562470 CAACCATAGAAGGCCACCAT Chr13:9562421..9562440 59.81 50
downstream ENSMUSE00000684771 Chr13:9562360..9562470 CAACCATAGAAGGCCACCAT Chr13:9562421..9562440 59.81 50
downstream ENSMUSE00000115141 Chr13:9567077..9567200 CAGCTTCCAAGCAAGAAACC Chr13:9567120..9567139 59.99 50
downstream ENSMUSE00000684770 Chr13:9567077..9567200 CAGCTTCCAAGCAAGAAACC Chr13:9567120..9567139 59.99 50
downstream ENSMUSE00000513357 Chr13:9567547..9567656 ACCAATCCCGAGGAGGTTTA Chr13:9567615..9567634 60.68 50
downstream ENSMUSE00000684769 Chr13:9567547..9567656 ACCAATCCCGAGGAGGTTTA Chr13:9567615..9567634 60.68 50
downstream ENSMUSE00000115135 Chr13:9567837..9567939 TATCCTCGTCACGGTCACAC Chr13:9567890..9567909 59.55 55
downstream ENSMUSE00000684768 Chr13:9567837..9567939 TATCCTCGTCACGGTCACAC Chr13:9567890..9567909 59.55 55
downstream ENSMUSE00000115133 Chr13:9570296..9570360 GAGCCCCACATCTTTCTTGA Chr13:9570345..9570364 60.19 50
downstream ENSMUSE00000684767 Chr13:9570296..9570360 GAGCCCCACATCTTTCTTGA Chr13:9570345..9570364 60.19 50
downstream ENSMUSE00000115157 Chr13:9574380..9574473 ATCAGCGAGTATGGGATGCT Chr13:9574429..9574448 59.68 50
downstream ENSMUSE00000684766 Chr13:9574380..9574473 ATCAGCGAGTATGGGATGCT Chr13:9574429..9574448 59.68 50
downstream ENSMUSE00000115137 Chr13:9574608..9574727 GCGAGGACAGGTTGACATCT Chr13:9574694..9574713 60.27 55
downstream ENSMUSE00000684764 Chr13:9574608..9574727 GCGAGGACAGGTTGACATCT Chr13:9574694..9574713 60.27 55
downstream ENSMUSE00000572019 Chr13:9576050..9576164 TCGAAGGCCTTTACTCTGGA Chr13:9576108..9576127 59.95 50
downstream ENSMUSE00000684763 Chr13:9576050..9576164 TCGAAGGCCTTTACTCTGGA Chr13:9576108..9576127 59.95 50
downstream ENSMUSE00000684762 Chr13:9583251..9583276 TTCTGAACACCTTCCATACCC Chr13:9583277..9583297 58.9 47.62
downstream ENSMUSE00000684793 Chr13:9583251..9583267 No primer for this exon
downstream ENSMUSE00000684792 Chr13:9591990..9592004 No primer for this exon
downstream ENSMUSE00000520435 Chr13:9600625..9600742 AGGCCTACATCCTGCACTGT Chr13:9600731..9600750 59.75 55
downstream ENSMUSE00000684791 Chr13:9600632..9600742 GCCTACATCCTGCACTGTGA Chr13:9600729..9600748 59.86 55
downstream ENSMUSE00000251706 Chr13:9603735..9603871 GGTCATGCCAGAGAGACCAT Chr13:9603859..9603878 60.08 55
downstream ENSMUSE00000684760 Chr13:9603735..9603871 GGTCATGCCAGAGAGACCAT Chr13:9603859..9603878 60.08 55
downstream ENSMUSE00000115134 Chr13:9605569..9605777 CATCAGGCCGTCCATCTTAC Chr13:9605694..9605713 60.48 55
downstream ENSMUSE00000684759 Chr13:9605569..9605777 CATCAGGCCGTCCATCTTAC Chr13:9605694..9605713 60.48 55
downstream ENSMUSE00000572018 Chr13:9608190..9608304 TGCTCATCCACTGGAAACTG Chr13:9608296..9608315 59.83 50
downstream ENSMUSE00000684758 Chr13:9608190..9608304 TGCTCATCCACTGGAAACTG Chr13:9608296..9608315 59.83 50
downstream ENSMUSE00000414418 Chr13:9609943..9610144 TTTGGGAAGGGTATTTGCTG Chr13:9610014..9610033 59.93 45
downstream ENSMUSE00000684757 Chr13:9609943..9610144 TTTGGGAAGGGTATTTGCTG Chr13:9610014..9610033 59.93 45
downstream ENSMUSE00000376391 Chr13:9613593..9613702 CTAGCCTGGGCAATCCTCTT Chr13:9613659..9613678 60.72 55
downstream ENSMUSE00000684754 Chr13:9613593..9613714 CTAGCCTGGGCAATCCTCTT Chr13:9613659..9613678 60.72 55
downstream ENSMUSE00000115159 Chr13:9614991..9615071 AGCAGATGGTCAGGAGTGGT Chr13:9615052..9615071 59.71 55
downstream ENSMUSE00000115148 Chr13:9621125..9621248 TCTTTTCTGCACGCTTGTGT Chr13:9621182..9621201 59.64 45
downstream ENSMUSE00000115136 Chr13:9621828..9621949 GCAATGTCGTTGCAATGTTC Chr13:9621929..9621948 60.13 45
downstream ENSMUSE00000115144 Chr13:9623003..9623114 TCTCTGGACCGAAGCAGTTT Chr13:9623067..9623086 59.99 50
downstream ENSMUSE00000251652 Chr13:9623204..9623313 AGTGTGTCAGGGTTGGAAGG Chr13:9623264..9623283 60 55
downstream ENSMUSE00000115129 Chr13:9627219..9627349 GAAGGGTAAAGCTCGCACTG Chr13:9627286..9627305 60.01 55
downstream ENSMUSE00000115127 Chr13:9633968..9634136 GCTCCATCACCGAATAGGAA Chr13:9634098..9634117 60.04 50
downstream ENSMUSE00000115145 Chr13:9636341..9636511 AAGCAAATTGCCAGGTTCAC Chr13:9636510..9636529 60.12 45
downstream ENSMUSE00000572009 Chr13:9646225..9646286 CATAGACAGTGGTGGGGTCA Chr13:9646261..9646280 59.39 55
downstream ENSMUSE00000115170 Chr13:9653849..9653906 CCCTTTCTACCAACCGGACT Chr13:9653871..9653890 60.35 55
downstream ENSMUSE00000115162 Chr13:9655883..9655957 GGGCCTTTTGTTTCTGGATT Chr13:9655935..9655954 60.3 45
downstream ENSMUSE00000572007 Chr13:9658491..9658665 AGAAAGCCCAGGTAGCCAGT Chr13:9658636..9658655 60.27 55
downstream ENSMUSE00000115153 Chr13:9661383..9661506 TGACACTTTTGTGGGCTCTG Chr13:9661502..9661521 59.87 50
downstream ENSMUSE00000618756 Chr13:9665024..9668171 GTTCCCCAACGGCTAGTACA Chr13:9666835..9666854 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCGCCTGTCACTCCTTCTAA Chr13:9505858..9505878 60.54 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCTCACCCTGCTGTTTTACC Chr13:9505797..9505817 59.74 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048264