Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6566
Trapped Gene
Ptpn23 (ENSMUSG00000036057)
Vector Insertion
Chr 9: 110291900 - 110291976
Public Clones YHB130 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 33% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000529294 (Chr9:110291977..110292294 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAAGGCTTCCTTCACCAACA Chr9:110292082..110292101 59.71 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000529294 (Chr9:110291977..110292294 -)
Downstram Exon
ENSMUSE00000529293 (Chr9:110291745..110291899 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAAGGCTTCCTTCACCAACA Chr9:110292082..110292101 59.71 45 ATGCGCTTTAGGTTTTGCAG Chr9:110291844..110291863 60.4 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000583195 Chr9:110310538..110310714 ACTTCCAGTCTGCGGTGAAG Chr9:110310541..110310560 60.44 55
upstream ENSMUSE00000583194 Chr9:110300625..110300699 CCAGAAGCCTACAACGAGGA Chr9:110300653..110300672 60.39 55
upstream ENSMUSE00000583193 Chr9:110296205..110296332 CCTTGGCCAGCTACACTACC Chr9:110296260..110296279 59.76 60
upstream ENSMUSE00000583192 Chr9:110295875..110295951 GATCTTCTCGGGCAAGTCTG Chr9:110295926..110295945 59.95 55
upstream ENSMUSE00000583191 Chr9:110295207..110295256 No primer for this exon
upstream ENSMUSE00000583190 Chr9:110294989..110295120 GACATGAGTCGCCAGATCCT Chr9:110295014..110295033 60.23 55
upstream ENSMUSE00000583189 Chr9:110294486..110294566 ATGTTGGACAACCGGAAGAG Chr9:110294514..110294533 59.97 50
upstream ENSMUSE00000583188 Chr9:110294271..110294402 GCCGTATCCAGAAAGACTGG Chr9:110294319..110294338 59.69 55
upstream ENSMUSE00000583187 Chr9:110294138..110294185 GCAACAGAAATTTGGGGAAC Chr9:110294140..110294159 59.41 45
upstream ENSMUSE00000583186 Chr9:110293713..110293769 GTGCCCTGGACAAGCTTAAT Chr9:110293734..110293753 59.2 50
upstream ENSMUSE00000583185 Chr9:110293548..110293606 AAGATGCACTTCGCTTTGCT Chr9:110293568..110293587 60.16 45
upstream ENSMUSE00000583184 Chr9:110293355..110293434 TGGATACACTCCAGCCTGTG Chr9:110293359..110293378 59.7 55
upstream ENSMUSE00000583183 Chr9:110293134..110293248 TGAAGCCCTTGCCAGTAAAC Chr9:110293217..110293236 60.25 50
upstream ENSMUSE00000583182 Chr9:110292974..110293039 ATGCTGGCCAAAATTGAAGA Chr9:110292992..110293011 60.58 40
upstream ENSMUSE00000529295 Chr9:110292547..110292692 AGCTGGACCCTGAGACAGTG Chr9:110292653..110292672 60.46 60
upstream ENSMUSE00000529294 Chr9:110291977..110292294 AAAGGCTTCCTTCACCAACA Chr9:110292082..110292101 59.71 45

*** Putative Vector Insertion (Chr 9: 110291900 - 110291976) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000529293 Chr9:110291745..110291899 ATGCGCTTTAGGTTTTGCAG Chr9:110291844..110291863 60.4 45
downstream ENSMUSE00000529292 Chr9:110291516..110291667 TTGGTCCAGCTCACTAAGCA Chr9:110291496..110291515 59.59 50
downstream ENSMUSE00000529291 Chr9:110291245..110291424 GCCTTCTTGGGACTTCTTCA Chr9:110291327..110291346 59.4 50
downstream ENSMUSE00000529290 Chr9:110289235..110291155 ACCACACGGTTGCTGTCATA Chr9:110289397..110289416 60.03 50
downstream ENSMUSE00000309333 Chr9:110288958..110289142 ATGGAGGTGCACAAGAGAGC Chr9:110288956..110288975 60.42 55
downstream ENSMUSE00000309312 Chr9:110288749..110288853 GGTCGCTGGTGCAAATAATG Chr9:110288757..110288776 61.42 50
downstream ENSMUSE00000309292 Chr9:110288522..110288660 TTTCCTGCAGCATGTGTTTC Chr9:110288502..110288521 59.85 45
downstream ENSMUSE00000309269 Chr9:110288318..110288431 CTCCACATGTCTCACCAACG Chr9:110288365..110288384 60.15 55
downstream ENSMUSE00000331626 Chr9:110287593..110288236 GCTAGCTGGTGGAAGACCTG Chr9:110288047..110288066 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGGTCTCTTTTAATCGCCTTG Chr9:110291914..110291935 60.08 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGGAAAGGCTTGGAACTAGG Chr9:110291933..110291953 60.07 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036057