Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9466
Trapped Gene
Cbfa2t2 (ENSMUSG00000038533)
Vector Insertion
Chr 2: 154343444 - 154343561
Public Clones RRD128 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000681332 (Chr2:154343445..154343560 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCCTCACTGTTCCCCTTATG Chr2:154343540..154343559 59.4 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000681332 (Chr2:154343445..154343560 +)
Downstram Exon
ENSMUSE00000709120 (Chr2:154343445..154343698 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCCTCACTGTTCCCCTTATG Chr2:154343540..154343559 59.4 55 GGTTCCCGATACAGGTGAGA Chr2:154343651..154343670 59.93 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000639806 Chr2:154262217..154262372 No primer for this exon
upstream ENSMUSE00000712948 Chr2:154262254..154262372 No primer for this exon
upstream ENSMUSE00000722077 Chr2:154262254..154262372 No primer for this exon
upstream ENSMUSE00000681333 Chr2:154262271..154262372 No primer for this exon
upstream ENSMUSE00000681316 Chr2:154262580..154262784 ATTGGAGCGACGAGTGGTAG Chr2:154262720..154262739 60.28 55
upstream ENSMUSE00000439463 Chr2:154326136..154326279 ACCCCTCCCACCAATAAATC Chr2:154326221..154326240 59.88 50
upstream ENSMUSE00000681307 Chr2:154326136..154326279 ACCCCTCCCACCAATAAATC Chr2:154326221..154326240 59.88 50
upstream ENSMUSE00000681306 Chr2:154330289..154330530 CCTCCACATCGTCAGCACTA Chr2:154330370..154330389 59.85 55
upstream ENSMUSE00000709093 Chr2:154330289..154330530 CCTCCACATCGTCAGCACTA Chr2:154330370..154330389 59.85 55
upstream ENSMUSE00000719439 Chr2:154330289..154330530 CCTCCACATCGTCAGCACTA Chr2:154330370..154330389 59.85 55
upstream ENSMUSE00000555056 Chr2:154336244..154336333 TTCGTCCATTTGTGATTCCA Chr2:154336305..154336324 59.9 40
upstream ENSMUSE00000712771 Chr2:154336244..154336333 TTCGTCCATTTGTGATTCCA Chr2:154336305..154336324 59.9 40
upstream ENSMUSE00000720844 Chr2:154336244..154336333 TTCGTCCATTTGTGATTCCA Chr2:154336305..154336324 59.9 40
upstream ENSMUSE00000555050 Chr2:154341553..154341734 CCAGTATCGCATCTCCTGCT Chr2:154341656..154341675 60.38 55
upstream ENSMUSE00000681313 Chr2:154341553..154341734 CCAGTATCGCATCTCCTGCT Chr2:154341656..154341675 60.38 55

*** Putative Vector Insertion (Chr 2: 154343444 - 154343561) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000681312 Chr2:154343445..154343698 GGTTCCCGATACAGGTGAGA Chr2:154343651..154343670 59.93 55
downstream ENSMUSE00000681332 Chr2:154343445..154343560 GCGGTTCAGGAGGAACTGTA Chr2:154343494..154343513 60.26 55
downstream ENSMUSE00000709120 Chr2:154343445..154343698 GGTTCCCGATACAGGTGAGA Chr2:154343651..154343670 59.93 55
downstream ENSMUSE00000720654 Chr2:154343445..154343698 GGTTCCCGATACAGGTGAGA Chr2:154343651..154343670 59.93 55
downstream ENSMUSE00000327832 Chr2:154346887..154346972 CCTTTCTGTCAAACGGTGGT Chr2:154346942..154346961 60.01 50
downstream ENSMUSE00000681330 Chr2:154346887..154346972 CCTTTCTGTCAAACGGTGGT Chr2:154346942..154346961 60.01 50
downstream ENSMUSE00000327825 Chr2:154349640..154349835 TAAACCGCCGTTTCCAATAG Chr2:154349754..154349773 59.96 45
downstream ENSMUSE00000681325 Chr2:154349640..154349835 TAAACCGCCGTTTCCAATAG Chr2:154349754..154349773 59.96 45
downstream ENSMUSE00000639805 Chr2:154350250..154350443 CAGACCGTGTGTTTTGCATC Chr2:154350339..154350358 60.16 50
downstream ENSMUSE00000327816 Chr2:154354573..154354641 CTGGTAAATTCCCGCTGAGA Chr2:154354597..154354616 60.21 50
downstream ENSMUSE00000681322 Chr2:154354573..154354641 CTGGTAAATTCCCGCTGAGA Chr2:154354597..154354616 60.21 50
downstream ENSMUSE00000327808 Chr2:154356958..154357148 CTGCTCCATTCGAGCTCTCT Chr2:154357076..154357095 59.85 55
downstream ENSMUSE00000681320 Chr2:154356958..154357148 CTGCTCCATTCGAGCTCTCT Chr2:154357076..154357095 59.85 55
downstream ENSMUSE00000681311 Chr2:154356961..154357148 CTGCTCCATTCGAGCTCTCT Chr2:154357076..154357095 59.85 55
downstream ENSMUSE00000681335 Chr2:154356961..154357148 CTGCTCCATTCGAGCTCTCT Chr2:154357076..154357095 59.85 55
downstream ENSMUSE00000505140 Chr2:154360620..154365092 GCCTGCTACCAGTCTTCAGG Chr2:154361292..154361311 60.01 60
downstream ENSMUSE00000681310 Chr2:154360620..154361490 GCCTGCTACCAGTCTTCAGG Chr2:154361292..154361311 60.01 60
downstream ENSMUSE00000681319 Chr2:154360620..154365090 GCCTGCTACCAGTCTTCAGG Chr2:154361292..154361311 60.01 60
downstream ENSMUSE00000681338 Chr2:154360620..154365090 GCCTGCTACCAGTCTTCAGG Chr2:154361292..154361311 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTCCTGAACCGCCTTAATC Chr2:154343480..154343500 60.95 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTTTCTTCTACAGGAGGGACGA Chr2:154343433..154343455 59.75 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000038533