Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3257
Trapped Gene
Rnf38 (ENSMUSG00000035696)
Vector Insertion
Chr 4: 44142529 - 44144415
Public Clones AK0251 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 95% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000373638 (Chr4:44144416..44144515 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTAACCACGAGTTCCATGC Chr4:44144441..44144460 59.57 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000373638 (Chr4:44144416..44144515 -)
Downstram Exon
ENSMUSE00000674570 (Chr4:44142292..44142528 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTAACCACGAGTTCCATGC Chr4:44144441..44144460 59.57 50 AGGCTGGTCACTCTGAATCG Chr4:44142437..44142456 60.41 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000527467 Chr4:44181115..44181211 No primer for this exon
upstream ENSMUSE00000674574 Chr4:44180499..44180823 GGCGAGCAGTCACAATAGGA Chr4:44180559..44180578 61.35 55
upstream ENSMUSE00000632786 Chr4:44180190..44180387 ACGCAGGTGAAGTGATGATG Chr4:44180324..44180343 59.71 50
upstream ENSMUSE00000419583 Chr4:44171775..44171924 GGCCAATTCAGCACCTCTAC Chr4:44171894..44171913 59.7 55
upstream ENSMUSE00000674573 Chr4:44171775..44171815 CCATTCAAGAGGATGCTCACT Chr4:44171792..44171812 59.3 47.62
upstream ENSMUSE00000674571 Chr4:44167513..44167605 TTCAGTCGTTTTCTGAGTTTGG Chr4:44167571..44167592 59.4 40.91
upstream ENSMUSE00000527488 Chr4:44165232..44165425 GGGAACGCTGTAACACACCT Chr4:44165249..44165268 60.03 55
upstream ENSMUSE00000660803 Chr4:44165232..44165425 GGGAACGCTGTAACACACCT Chr4:44165249..44165268 60.03 55
upstream ENSMUSE00000527485 Chr4:44161897..44162110 CGAATGTATCTCCCCGTCTG Chr4:44161957..44161976 60.47 55
upstream ENSMUSE00000527483 Chr4:44156320..44156487 ACCTCCCCGTCTGTAGTGTG Chr4:44156329..44156348 60.03 60
upstream ENSMUSE00000527480 Chr4:44155167..44155337 TGCTTCAGGCATGTTCAGTT Chr4:44155317..44155336 59.44 45
upstream ENSMUSE00000527478 Chr4:44151542..44151703 ATGACCCTTTGCATCAGGAG Chr4:44151557..44151576 60.07 50
upstream ENSMUSE00000527475 Chr4:44150427..44150533 TCGGAGACTCACAGGACGTA Chr4:44150494..44150513 59.42 55
upstream ENSMUSE00000527473 Chr4:44147762..44147846 CCCAACCTTCAGCTTTGAAT Chr4:44147797..44147816 59.17 45
upstream ENSMUSE00000527471 Chr4:44146512..44146633 CCTGTTAAACTTGGCGGAGA Chr4:44146612..44146631 60.24 50
upstream ENSMUSE00000373638 Chr4:44144416..44144515 TGTAACCACGAGTTCCATGC Chr4:44144441..44144460 59.57 50

*** Putative Vector Insertion (Chr 4: 44142529 - 44144415) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000674570 Chr4:44142292..44142528 AGGCTGGTCACTCTGAATCG Chr4:44142437..44142456 60.41 55
downstream ENSMUSE00000632785 Chr4:44139087..44142528 GTGTGAAGAGGCCCAAATGT Chr4:44139460..44139479 59.97 50
downstream ENSMUSE00000488423 Chr4:44139085..44142528 GTGTGAAGAGGCCCAAATGT Chr4:44139460..44139479 59.97 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGTAACCACGAGTTCCATGC Chr4:44144439..44144459 59.57 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTAACCACGAGTTCCATGC Chr4:44144439..44144459 59.57 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000035696