Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5288
Trapped Gene
Mtap4 (ENSMUSG00000032479)
Vector Insertion
Chr 9: 109902345 - 109928604
Public Clones YHD088 (baygenomics) RRD072 (baygenomics) YTB020 (baygenomics) W061E06 (ggtc)
Private Clones OST375669 (lexicon) OST301288 (lexicon) OST283965 (lexicon) OST280375 (lexicon)
OST224622 (lexicon) OST208998 (lexicon) OST195866 (lexicon) OST58424 (lexicon)
Severity of mutation (?) Insertion after 9% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000583223 (Chr9:109902276..109902344 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TAGCCAATGGTGATCATGGA Chr9:109902303..109902322 59.88 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000583223 (Chr9:109902276..109902344 +)
Downstram Exon
ENSMUSE00000583222 (Chr9:109928605..109928727 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TAGCCAATGGTGATCATGGA Chr9:109902303..109902322 59.88 45 TAACACTTGCTGAGGCTGGA Chr9:109928714..109928733 59.59 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000690141 Chr9:109833962..109834444 CGCCTGACACTAGCATCCTT Chr9:109834002..109834021 60.42 55
upstream ENSMUSE00000583224 Chr9:109881354..109881595 GCAGTCGCAGTGGTACAGAA Chr9:109881354..109881373 60.06 55
upstream ENSMUSE00000583223 Chr9:109902276..109902344 TAGCCAATGGTGATCATGGA Chr9:109902303..109902322 59.88 45

*** Putative Vector Insertion (Chr 9: 109902345 - 109928604) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000583222 Chr9:109928605..109928727 TAACACTTGCTGAGGCTGGA Chr9:109928714..109928733 59.59 50
downstream ENSMUSE00000583221 Chr9:109930183..109930296 ATCACGGTGCTCGTTAAAGG Chr9:109930208..109930227 60.13 50
downstream ENSMUSE00000583220 Chr9:109934603..109934737 TGAGATACAACAGCCGTGGA Chr9:109934651..109934670 60.26 50
downstream ENSMUSE00000583219 Chr9:109936877..109938010 TTTGGGGGATGTCGTATCAT Chr9:109937256..109937275 60.01 45
downstream ENSMUSE00000583218 Chr9:109939246..109939359 GGCGTTTCCTTCTGCTCTAA Chr9:109939333..109939352 59.59 50
downstream ENSMUSE00000634040 Chr9:109954667..109956026 AAGGTGACCGGAGGTTTCTT Chr9:109954900..109954919 59.97 50
downstream ENSMUSE00000690134 Chr9:109965521..109965627 GCGGGGTAGTGATGTCATTT Chr9:109965589..109965608 59.82 50
downstream ENSMUSE00000583216 Chr9:109966732..109966953 TGTTTTGGCTTTCGATGTTG Chr9:109966785..109966804 59.71 40
downstream ENSMUSE00000583215 Chr9:109969989..109970172 GGGTGGTTTTAGGTCCAGGT Chr9:109970082..109970101 60.09 55
downstream ENSMUSE00000583214 Chr9:109971028..109971087 TTTCCCCTCAGTCTTGATGC Chr9:109971050..109971069 60.19 50
downstream ENSMUSE00000583213 Chr9:109971197..109971489 CTGTAGAGCCGACCTTGGAG Chr9:109971460..109971479 60.01 60
downstream ENSMUSE00000219958 Chr9:109973530..109973643 GTTTCTGTGCACTCGCAATG Chr9:109973632..109973651 60.46 50
downstream ENSMUSE00000583212 Chr9:109975117..109975209 GTCCTTGGAACCACACTTGG Chr9:109975182..109975201 60.4 55
downstream ENSMUSE00000583211 Chr9:109980507..109980588 CCACACTTGGAGGAGACCTT Chr9:109980562..109980581 59.15 55
downstream ENSMUSE00000583210 Chr9:109982285..109982397 AAGTGGCCCACGTTATCAAG Chr9:109982378..109982397 59.99 50
downstream ENSMUSE00000529394 Chr9:109983925..109984114 ATCTGGCTGTCCAAGGTCTG Chr9:109984106..109984125 60.26 55
downstream ENSMUSE00000583202 Chr9:109984239..109986450 GGCTTCAGCCTGCAAACTAC Chr9:109985058..109985077 60.02 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTATCCATCTAATCGCCTTGC Chr9:109923387..109923408 58.82 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCAGAAGAACCCTATGGAAGG Chr9:109923304..109923325 59.94 52.38 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032479