Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1531
Trapped Gene
Bcar3 (ENSMUSG00000028121)
Vector Insertion
Chr 3: 122158011 - 122207844
Public Clones CC0525 (sanger) IST10051E5 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 14% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000263246 (Chr3:122157971..122158010 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTTCTGGACCCAACTCTGGA Chr3:122157981..122158000 60.23 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000263246 (Chr3:122157971..122158010 +)
Downstram Exon
ENSMUSE00000563764 (Chr3:122207845..122207973 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTTCTGGACCCAACTCTGGA Chr3:122157981..122158000 60.23 55 GTCCATGATGTGCCTCTCCT Chr3:122207874..122207893 60.08 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000333208 Chr3:122122716..122123101 CTTCTCGGGGGAAGATAAGG Chr3:122122732..122122751 60.03 55
upstream ENSMUSE00000263252 Chr3:122129363..122129672 TCCATACGGTCCTGTGACAA Chr3:122129551..122129570 59.96 50
upstream ENSMUSE00000263246 Chr3:122157971..122158010 CTTCTGGACCCAACTCTGGA Chr3:122157981..122158000 60.23 55

*** Putative Vector Insertion (Chr 3: 122158011 - 122207844) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000563764 Chr3:122207845..122207973 GTCCATGATGTGCCTCTCCT Chr3:122207874..122207893 60.08 55
downstream ENSMUSE00000176418 Chr3:122211044..122211489 TCCTATTGATGGGCTGGAAG Chr3:122211326..122211345 60.03 50
downstream ENSMUSE00000176433 Chr3:122214137..122214240 CAGGTGACTCTCCGACTGGT Chr3:122214236..122214255 60.31 60
downstream ENSMUSE00000176429 Chr3:122215269..122215921 TCATTGGGTCTGAATGACGA Chr3:122215794..122215813 60.05 45
downstream ENSMUSE00000176427 Chr3:122222181..122222296 CTGCCGTCCATGAGGTAAAG Chr3:122222276..122222295 60.65 55
downstream ENSMUSE00000176423 Chr3:122226087..122226258 CGCCACCTGGATGATCTTAT Chr3:122226189..122226208 59.92 50
downstream ENSMUSE00000263191 Chr3:122227842..122227953 ATGGCTGTCTGCGTGTAGTG Chr3:122227903..122227922 59.93 55
downstream ENSMUSE00000176416 Chr3:122228205..122228417 ACATGTCGGTCCCTTCAAAA Chr3:122228309..122228328 60.35 45
downstream ENSMUSE00000332685 Chr3:122232500..122233098 GGGCTGTTAGGATCTGGTTG Chr3:122232634..122232653 59.55 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTCCCCCACTGGCCTATAAT Chr3:122170046..122170066 60.04 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGGTTCGTGACTGGGAAAA Chr3:122170056..122170076 61.06 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028121