Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI21607
Trapped Gene
Gabpb2 (ENSMUSG00000038766)
Vector Insertion
Chr 3: 95020191 - 95021510
Public Clones (sanger) (ggtc) 5SD059B05 (ggtc) 5SD032C06 (ggtc)
Private Clones OST324174 (lexicon) OST324146 (lexicon) OST260620 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000672413 (Chr3:95021511..95021631 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTGAAAAGGCCGAAAAGTGA Chr3:95021600..95021619 60.23 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000672413 (Chr3:95021511..95021631 -)
Downstram Exon
ENSMUSE00000672416 (Chr3:95020136..95020190 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTGAAAAGGCCGAAAAGTGA Chr3:95021600..95021619 60.23 45 GTGGAAGCCACAGGACAACT Chr3:95020122..95020141 60.16 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000672406 Chr3:95021511..95021676 GTGAAAAGGCCGAAAAGTGA Chr3:95021600..95021619 60.23 45
upstream ENSMUSE00000672413 Chr3:95021511..95021631 GTGAAAAGGCCGAAAAGTGA Chr3:95021600..95021619 60.23 45
upstream ENSMUSE00000672417 Chr3:95021511..95021825 GTGAAAAGGCCGAAAAGTGA Chr3:95021600..95021619 60.23 45

*** Putative Vector Insertion (Chr 3: 95020191 - 95021510) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000672416 Chr3:95020136..95020190 GTGGAAGCCACAGGACAACT Chr3:95020122..95020141 60.16 55
downstream ENSMUSE00000420483 Chr3:95012762..95012859 TCCCAGTACAGCCAAGAACA Chr3:95012814..95012833 59.29 50
downstream ENSMUSE00000672415 Chr3:95012762..95012858 TCCCAGTACAGCCAAGAACA Chr3:95012814..95012833 59.29 50
downstream ENSMUSE00000709675 Chr3:95010385..95010524 CCCAAGTCCACCAGAGACAT Chr3:95010451..95010470 59.96 55
downstream ENSMUSE00000710889 Chr3:95010385..95010524 CCCAAGTCCACCAGAGACAT Chr3:95010451..95010470 59.96 55
downstream ENSMUSE00000720201 Chr3:95010385..95010524 CCCAAGTCCACCAGAGACAT Chr3:95010451..95010470 59.96 55
downstream ENSMUSE00000253802 Chr3:95008563..95008730 AGCTCGAAGGAGCACTTCTG Chr3:95008637..95008656 59.89 55
downstream ENSMUSE00000672409 Chr3:95008563..95008730 AGCTCGAAGGAGCACTTCTG Chr3:95008637..95008656 59.89 55
downstream ENSMUSE00000494767 Chr3:95007653..95007847 CATGTCCTTTGCGTTCACAT Chr3:95007796..95007815 59.57 45
downstream ENSMUSE00000637761 Chr3:95007653..95007847 CATGTCCTTTGCGTTCACAT Chr3:95007796..95007815 59.57 45
downstream ENSMUSE00000672404 Chr3:95006935..95007847 ACACACCTGAAGCATGACCA Chr3:95007625..95007644 60.16 50
downstream ENSMUSE00000253781 Chr3:95004063..95004213 TGAACGGAGCAGTCACAGTC Chr3:95004110..95004129 60.03 55
downstream ENSMUSE00000566319 Chr3:95004040..95004213 TGAACGGAGCAGTCACAGTC Chr3:95004110..95004129 60.03 55
downstream ENSMUSE00000637758 Chr3:95003999..95004037 No primer for this exon
downstream ENSMUSE00000253769 Chr3:94994475..94994660 CTGGGTCGAGGAGTCAAGAG Chr3:94994589..94994608 59.98 60
downstream ENSMUSE00000253759 Chr3:94993076..94993206 GTCTCCTCTGCAACCTGACC Chr3:94993148..94993167 59.84 60
downstream ENSMUSE00000420468 Chr3:94991173..94992897 CTGTACTCCTGGGCTCTTCG Chr3:94992808..94992827 60.01 60
downstream ENSMUSE00000637762 Chr3:94985695..94992897 TCTACCCATCAGCAGCACAG Chr3:94990832..94990851 60.01 55
downstream ENSMUSE00000672412 Chr3:94985688..94992897 TCTACCCATCAGCAGCACAG Chr3:94990832..94990851 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGAATAGGTGAGGGGGAAAG Chr3:95021496..95021516 59.76 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGAATAGGTGAGGGGGAAAG Chr3:95021496..95021516 59.76 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AGTTAATCGCCTTGCAGCAC Chr3:95021564..95021584 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000038766