Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26456
Trapped Gene
Agl (ENSMUSG00000033400)
Vector Insertion
Chr 3: 116449623 - 116453315
Public Clones not available
Private Clones OST116738 (lexicon)
Severity of mutation (?) Insertion after 93% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000323448 (Chr3:116453316..116453413 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACTGCTGAGAAGGCTTGGAA Chr3:116453379..116453398 60.13 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000323448 (Chr3:116453316..116453413 -)
Downstram Exon
ENSMUSE00000323446 (Chr3:116449535..116449622 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACTGCTGAGAAGGCTTGGAA Chr3:116453379..116453398 60.13 50 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000670113 Chr3:116510946..116511084 No primer for this exon
upstream ENSMUSE00000670112 Chr3:116510186..116510335 GAATCCTCCAGAAGCCAAAA Chr3:116510267..116510286 59.24 45
upstream ENSMUSE00000670111 Chr3:116496530..116496740 GTTCCGATTAGGCCCAACTT Chr3:116496708..116496727 60.32 50
upstream ENSMUSE00000670110 Chr3:116494936..116495102 TAGGACCCTTCGATGAGTGG Chr3:116494967..116494986 60.06 55
upstream ENSMUSE00000670109 Chr3:116493924..116494127 CCTTGCCGATCAGTTAGAGC Chr3:116494047..116494066 59.98 55
upstream ENSMUSE00000670108 Chr3:116491444..116491625 AACACCCGGAATCTGCATAC Chr3:116491582..116491601 59.82 50
upstream ENSMUSE00000670107 Chr3:116491189..116491300 TCCCAAGGATTCAACTCTGG Chr3:116491250..116491269 60.04 50
upstream ENSMUSE00000670105 Chr3:116490148..116490271 ACACTGCTCTGGCGACTTTT Chr3:116490159..116490178 60.06 50
upstream ENSMUSE00000670103 Chr3:116489637..116489739 CAGCTGCAATTGAAGAGTGC Chr3:116489712..116489731 59.75 50
upstream ENSMUSE00000670100 Chr3:116489448..116489545 GCCATGGCCCTAAACTAGGA Chr3:116489480..116489499 61.32 55
upstream ENSMUSE00000670099 Chr3:116487978..116488117 CCTGATCCACCTCCCAGATA Chr3:116488050..116488069 59.88 55
upstream ENSMUSE00000670098 Chr3:116487371..116487558 TTGCGCTATGGGAATAAACC Chr3:116487486..116487505 59.93 45
upstream ENSMUSE00000670097 Chr3:116485438..116485561 CTGTTCACAGGAAGCGAAGA Chr3:116485488..116485507 59.16 50
upstream ENSMUSE00000670095 Chr3:116484506..116484669 GCGCGTATAACAGTCACGAA Chr3:116484641..116484660 59.9 50
upstream ENSMUSE00000670093 Chr3:116484161..116484262 TACGACGAGCTAGTGCCTCA Chr3:116484165..116484184 59.76 55
upstream ENSMUSE00000670092 Chr3:116483910..116484065 GTGCCATCAATAGGCTCCAT Chr3:116483940..116483959 59.92 50
upstream ENSMUSE00000670091 Chr3:116483644..116483794 CATCCACCAGTCTGTTGTGG Chr3:116483719..116483738 60 55
upstream ENSMUSE00000670090 Chr3:116482174..116482298 ATCAATGGAATGCCGAACAT Chr3:116482202..116482221 60.16 40
upstream ENSMUSE00000670089 Chr3:116481973..116482085 CACAAAGGGTCCCAATGAAT Chr3:116482028..116482047 59.65 45
upstream ENSMUSE00000670088 Chr3:116481537..116481671 GATTCTTCGGAACCACCTGA Chr3:116481616..116481635 60.05 50
upstream ENSMUSE00000670087 Chr3:116479447..116479577 TTGGCTGAGCTAAACCAGGTA Chr3:116479538..116479558 59.89 47.62
upstream ENSMUSE00000670086 Chr3:116475682..116475818 TTAATGTCCGTGTTGGCAGA Chr3:116475797..116475816 60.11 45
upstream ENSMUSE00000670085 Chr3:116475305..116475438 CAGATCCCACGCTACCTCAT Chr3:116475380..116475399 60.1 55
upstream ENSMUSE00000670084 Chr3:116474258..116474433 TTCAGAACGGATCCACCTTC Chr3:116474409..116474428 60.05 50
upstream ENSMUSE00000670083 Chr3:116471704..116471806 GCTGGTTACTGGACGCTACC Chr3:116471714..116471733 59.76 60
upstream ENSMUSE00000670082 Chr3:116461609..116461834 GCATTCAGGACTATTGCAGGA Chr3:116461698..116461718 60.23 47.62
upstream ENSMUSE00000323476 Chr3:116461157..116461268 ACCGAAACATGAAGGACGAG Chr3:116461158..116461177 60.11 50
upstream ENSMUSE00000323471 Chr3:116457791..116457926 GGAGGAAATCGCTTCAACTG Chr3:116457860..116457879 59.81 50
upstream ENSMUSE00000323461 Chr3:116456169..116456281 ATGGGTCTGCTGTGGAAATC Chr3:116456260..116456279 59.93 50
upstream ENSMUSE00000323364 Chr3:116454903..116455114 CTATGGTGCGTCGAGTCCTT Chr3:116454950..116454969 60.28 55
upstream ENSMUSE00000323448 Chr3:116453316..116453413 ACTGCTGAGAAGGCTTGGAA Chr3:116453379..116453398 60.13 50

*** Putative Vector Insertion (Chr 3: 116449623 - 116453315) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000323446 Chr3:116449535..116449622 No primer for this exon
downstream ENSMUSE00000323438 Chr3:116449298..116449431 GCAGTCTCTGGACCCATCAT Chr3:116449336..116449355 60.08 55
downstream ENSMUSE00000337361 Chr3:116442917..116447853 AGTAATGTGAAGGCGGTTGG Chr3:116443257..116443276 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGTGGGATACTTCCCCAGT Chr3:116450312..116450332 59.26 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGTGGGATACTTCCCCAGT Chr3:116450312..116450332 59.26 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000033400