Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2693
Trapped Gene
2810403A07Rik (ENSMUSG00000028060)
Vector Insertion
Chr 3: 88504437 - 88512701
Public Clones AL0335 (sanger) AK0047 (sanger) YHB244 (baygenomics) RRT159 (baygenomics)
A036A02 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 69% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000175571 (Chr3:88504183..88504436 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTTTCATTGGCACCTGGAGT Chr3:88504332..88504351 59.97 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000175571 (Chr3:88504183..88504436 +)
Downstram Exon
ENSMUSE00000175587 (Chr3:88512702..88512863 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTTTCATTGGCACCTGGAGT Chr3:88504332..88504351 59.97 50 TGTGAATCGCCTCTTCTGTG Chr3:88512821..88512840 59.98 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000175588 Chr3:88489749..88489809 No primer for this exon
upstream ENSMUSE00000290849 Chr3:88490266..88490488 TGCCAAGATCAATGCTATGC Chr3:88490422..88490441 59.8 45
upstream ENSMUSE00000175585 Chr3:88493097..88493225 CAATGACGTGCCTCTGACAT Chr3:88493168..88493187 59.71 50
upstream ENSMUSE00000175574 Chr3:88493546..88493625 GACGGTTCATGACGACTGAG Chr3:88493583..88493602 59.26 55
upstream ENSMUSE00000175578 Chr3:88496998..88497050 GGGACAGACACGGGAATTAG Chr3:88497025..88497044 59.4 55
upstream ENSMUSE00000175577 Chr3:88497343..88497506 TCCAACTTTCAATGGTGCAA Chr3:88497407..88497426 60.09 40
upstream ENSMUSE00000175575 Chr3:88500487..88500698 TTCTACGAGGGAAAGGCTCA Chr3:88500620..88500639 59.95 50
upstream ENSMUSE00000175581 Chr3:88502771..88502831 CCAAGAAGCTCTGCGAGAAT Chr3:88502800..88502819 59.72 50
upstream ENSMUSE00000175584 Chr3:88503873..88503930 No primer for this exon
upstream ENSMUSE00000175571 Chr3:88504183..88504436 GTTTCATTGGCACCTGGAGT Chr3:88504332..88504351 59.97 50

*** Putative Vector Insertion (Chr 3: 88504437 - 88512701) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000175587 Chr3:88512702..88512863 TGTGAATCGCCTCTTCTGTG Chr3:88512821..88512840 59.98 50
downstream ENSMUSE00000175586 Chr3:88513752..88513864 ATCCTGCGCCTTCTATCTCA Chr3:88513824..88513843 59.94 50
downstream ENSMUSE00000175576 Chr3:88514683..88514774 CCAGACCCATTCCTTTCATC Chr3:88514757..88514776 59.34 50
downstream ENSMUSE00000378006 Chr3:88515552..88515751 AATCCCTTCTCTGCCGTTTT Chr3:88515594..88515613 60.07 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGTGGCACATGGCATTTAAC Chr3:88510441..88510461 60.39 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTAGCGTGACTGGGAAAACC Chr3:88507484..88507504 59.6 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028060