Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI699
Trapped Gene
Gpbp1 (ENSMUSG00000032745)
Vector Insertion
Chr 13: 112257179 - 112277630
Public Clones CA0181 (sanger) DC0005 (sanger) AM0517 (sanger) AE0175 (sanger)
Ex335 (baygenomics) YHA328 (baygenomics) RRM010 (baygenomics) LRY034 (baygenomics)
M124E10 (ggtc) M124E10 (ggtc) W036A07 (ggtc)
Private Clones OST370964 (lexicon) OST281232 (lexicon) OST253400 (lexicon) OST198301 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000706092 (Chr13:112277631..112278123 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCTTGTGCAGTCCTTTTGGA Chr13:112277635..112277654 59.42 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000706092 (Chr13:112277631..112278123 -)
Downstram Exon
ENSMUSE00000316419 (Chr13:112257059..112257178 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCTTGTGCAGTCCTTTTGGA Chr13:112277635..112277654 59.42 45 AAGGCTTCAACACCTCATGG Chr13:112257130..112257149 60.11 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000120497 Chr13:112279926..112280047 GGCAAAAGGGGATTATTCAA Chr13:112280000..112280019 58.88 40
upstream ENSMUSE00000610285 Chr13:112279926..112280236 GGGACTGAGACTGGTTGTGG Chr13:112280033..112280052 60.56 60
upstream ENSMUSE00000316427 Chr13:112277631..112278578 TGGTTGAATTTGGCGTATGA Chr13:112278558..112278577 59.93 40
upstream ENSMUSE00000706092 Chr13:112277631..112278123 TCTTGTGCAGTCCTTTTGGA Chr13:112277635..112277654 59.42 45

*** Putative Vector Insertion (Chr 13: 112257179 - 112277630) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000316419 Chr13:112257059..112257178 AAGGCTTCAACACCTCATGG Chr13:112257130..112257149 60.11 50
downstream ENSMUSE00000709405 Chr13:112257059..112257178 AAGGCTTCAACACCTCATGG Chr13:112257130..112257149 60.11 50
downstream ENSMUSE00000316480 Chr13:112243581..112243704 GGACGTCCAATACCAGAATCA Chr13:112243567..112243587 59.81 47.62
downstream ENSMUSE00000441336 Chr13:112243232..112243455 TGCTACGAGAACGGGAATTT Chr13:112243323..112243342 59.71 45
downstream ENSMUSE00000316470 Chr13:112239141..112239207 AAACACCCGCAGCTAAAGAT Chr13:112239122..112239141 58.86 45
downstream ENSMUSE00000316408 Chr13:112238104..112238163 GTGTGTGTCTGGGCGTGTAG Chr13:112238120..112238139 60.23 60
downstream ENSMUSE00000369274 Chr13:112230840..112231024 CCTGCTACTGGGAATCCAGA Chr13:112230906..112230925 60.21 55
downstream ENSMUSE00000316459 Chr13:112229312..112229452 TTCTTGGCCGTTGACTTAAAA Chr13:112229321..112229341 59.74 38.1
downstream ENSMUSE00000316453 Chr13:112228165..112228332 GGCGAAGAAGAATTTGAACG Chr13:112228285..112228304 59.82 45
downstream ENSMUSE00000679708 Chr13:112226605..112226792 TGTGGAAAAGTCGAAGAACG Chr13:112226622..112226641 58.9 45
downstream ENSMUSE00000568902 Chr13:112223756..112223858 GGGAGCACATGTTTCATCATT Chr13:112223779..112223799 59.81 42.86
downstream ENSMUSE00000679704 Chr13:112216369..112216859 ATGTTCAACACAGCCCAACA Chr13:112216501..112216520 60.01 45
downstream ENSMUSE00000610286 Chr13:112216140..112216859 CACTCTGCTCCGGTTTTAGC Chr13:112216158..112216177 60.01 55
downstream ENSMUSE00000568901 Chr13:112215890..112216859 CACTCTGCTCCGGTTTTAGC Chr13:112216158..112216177 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCCCCAATAAAAGGTGAGGT Chr13:112271615..112271635 60.05 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCCCCAATAAAAGGTGAGGT Chr13:112271615..112271635 60.05 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GTCTGAACACTGGCTGGCTCA Chr13:112272132..112272153 63.92 57.14 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 AAAACCAAGCTCTCCGTGAC Chr13:112272067..112272087 59.33 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032745