Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI18463
Trapped Gene
Bptf (ENSMUSG00000040481)
Vector Insertion
Chr 11: 106972950 - 106992587
Public Clones CMHD-GT_460G8-3 (cmhd) (cmhd) (cmhd) IST14980E4 (tigm) IST14980F4 (tigm)
IST15055C10 (tigm) IST14923G9 (tigm) IST14811C11 (tigm)
Private Clones OST422952 (lexicon) OST280617 (lexicon) OST262127 (lexicon) OST204219 (lexicon)
OST194467 (lexicon) OST147133 (lexicon) OST43264 (lexicon)
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000486355 (Chr11:106992588..106993441 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GATGACCACGAGAGTGACGA Chr11:106992809..106992828 59.83 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000486355 (Chr11:106992588..106993441 -)
Downstram Exon
ENSMUSE00000108627 (Chr11:106972127..106972949 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GATGACCACGAGAGTGACGA Chr11:106992809..106992828 59.83 55 AAGCAAAAAGGGGACAACCT Chr11:106972741..106972760 59.98 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000486355 Chr11:106992588..106993441 GATGACCACGAGAGTGACGA Chr11:106992809..106992828 59.83 55
upstream ENSMUSE00000714292 Chr11:106992588..106993441 GATGACCACGAGAGTGACGA Chr11:106992809..106992828 59.83 55

*** Putative Vector Insertion (Chr 11: 106972950 - 106992587) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000108627 Chr11:106972127..106972949 AAGCAAAAAGGGGACAACCT Chr11:106972741..106972760 59.98 45
downstream ENSMUSE00000108626 Chr11:106960880..106961103 CGCTAGGAAGGACTTGTTGC Chr11:106960868..106960887 60.01 55
downstream ENSMUSE00000108629 Chr11:106957030..106957239 CCCTCATGCTTGTCCTTTTC Chr11:106957127..106957146 59.67 50
downstream ENSMUSE00000576188 Chr11:106956316..106956504 GATGCCACCTTCTTCTCTGC Chr11:106956317..106956336 59.96 55
downstream ENSMUSE00000671086 Chr11:106948026..106948211 CGCTGCCTTAGCAGAGTCAC Chr11:106948065..106948084 61.28 60
downstream ENSMUSE00000108620 Chr11:106943827..106944014 CAGGGGACTCGGAAACTTCT Chr11:106943945..106943964 60.62 55
downstream ENSMUSE00000364449 Chr11:106942530..106942885 GTGAACAGACCCGTTCCATT Chr11:106942609..106942628 59.83 50
downstream ENSMUSE00000396339 Chr11:106942037..106942168 GAACGGCCTTGATCCAATTA Chr11:106942124..106942143 59.9 45
downstream ENSMUSE00000711588 Chr11:106939834..106939963 TGGTGCTTCACTGGAAATGT Chr11:106939813..106939832 59.14 45
downstream ENSMUSE00000712453 Chr11:106939834..106939963 TGGTGCTTCACTGGAAATGT Chr11:106939813..106939832 59.14 45
downstream ENSMUSE00000671053 Chr11:106938974..106939082 AACGTGCGTCTTGCTAATCC Chr11:106939016..106939035 60.28 50
downstream ENSMUSE00000671081 Chr11:106938974..106939082 AACGTGCGTCTTGCTAATCC Chr11:106939016..106939035 60.28 50
downstream ENSMUSE00000671052 Chr11:106937836..106938015 TGGACTTCGTGGACTTTTCC Chr11:106937932..106937951 60.09 50
downstream ENSMUSE00000671080 Chr11:106937836..106938015 TGGACTTCGTGGACTTTTCC Chr11:106937932..106937951 60.09 50
downstream ENSMUSE00000646795 Chr11:106933997..106934047 CCAAAGGTCGGTCTAGGAGA Chr11:106933987..106934006 59.28 55
downstream ENSMUSE00000671050 Chr11:106933997..106936304 GTGCTGCTATCGTCCTGTGA Chr11:106935544..106935563 60.02 55
downstream ENSMUSE00000671079 Chr11:106933997..106936304 GTGCTGCTATCGTCCTGTGA Chr11:106935544..106935563 60.02 55
downstream ENSMUSE00000671078 Chr11:106929589..106929713 TGTCCGTGTAGACCCTCCTC Chr11:106929568..106929587 60.11 60
downstream ENSMUSE00000710104 Chr11:106929589..106929713 TGTCCGTGTAGACCCTCCTC Chr11:106929568..106929587 60.11 60
downstream ENSMUSE00000719142 Chr11:106929589..106929713 TGTCCGTGTAGACCCTCCTC Chr11:106929568..106929587 60.11 60
downstream ENSMUSE00000352211 Chr11:106928441..106928569 CCCACATCACGCCTCTTAAT Chr11:106928493..106928512 59.96 50
downstream ENSMUSE00000671048 Chr11:106928441..106928569 CCCACATCACGCCTCTTAAT Chr11:106928493..106928512 59.96 50
downstream ENSMUSE00000390684 Chr11:106927260..106927410 CTCAGCAAAAGCCCTGATCT Chr11:106927240..106927259 59.57 50
downstream ENSMUSE00000671046 Chr11:106927260..106927410 CTCAGCAAAAGCCCTGATCT Chr11:106927240..106927259 59.57 50
downstream ENSMUSE00000344737 Chr11:106926982..106927024 CTGCTGCTTGAGCCTTTTCT Chr11:106926974..106926993 59.9 50
downstream ENSMUSE00000671045 Chr11:106926982..106927024 CTGCTGCTTGAGCCTTTTCT Chr11:106926974..106926993 59.9 50
downstream ENSMUSE00000404413 Chr11:106923850..106924096 CACGTGGCAAAAGTTTGATG Chr11:106923854..106923873 60.15 45
downstream ENSMUSE00000671044 Chr11:106923850..106924096 CACGTGGCAAAAGTTTGATG Chr11:106923854..106923873 60.15 45
downstream ENSMUSE00000671067 Chr11:106923364..106923525 CCCGTAATTTGGAACGTCTG Chr11:106923437..106923456 60.36 50
downstream ENSMUSE00000358525 Chr11:106922998..106923149 CCTGGGCTGGAATGAAGTAA Chr11:106923039..106923058 60.07 50
downstream ENSMUSE00000671043 Chr11:106922998..106923149 CCTGGGCTGGAATGAAGTAA Chr11:106923039..106923058 60.07 50
downstream ENSMUSE00000671041 Chr11:106921786..106921894 GTGTTCGAATGATCGCCTTT Chr11:106921782..106921801 60.08 45
downstream ENSMUSE00000714899 Chr11:106921786..106921894 GTGTTCGAATGATCGCCTTT Chr11:106921782..106921801 60.08 45
downstream ENSMUSE00000720302 Chr11:106921786..106921894 GTGTTCGAATGATCGCCTTT Chr11:106921782..106921801 60.08 45
downstream ENSMUSE00000353016 Chr11:106919948..106920165 TCACAACTTGTTGGGGTGTG Chr11:106920123..106920142 60.45 50
downstream ENSMUSE00000671066 Chr11:106919948..106920165 TCACAACTTGTTGGGGTGTG Chr11:106920123..106920142 60.45 50
downstream ENSMUSE00000393473 Chr11:106917186..106917420 CCAGTAGTCTGCCCTTGTCC Chr11:106917346..106917365 59.72 60
downstream ENSMUSE00000671065 Chr11:106917186..106917420 CCAGTAGTCTGCCCTTGTCC Chr11:106917346..106917365 59.72 60
downstream ENSMUSE00000490446 Chr11:106915770..106916632 AATTGGAATCGGCTGTGAAG Chr11:106916204..106916223 60.07 45
downstream ENSMUSE00000671064 Chr11:106915770..106916632 AATTGGAATCGGCTGTGAAG Chr11:106916204..106916223 60.07 45
downstream ENSMUSE00000324110 Chr11:106914537..106914619 CTCTTTCAGCTGGAGTCATGG Chr11:106914528..106914548 60 52.38
downstream ENSMUSE00000671063 Chr11:106914537..106914619 CTCTTTCAGCTGGAGTCATGG Chr11:106914528..106914548 60 52.38
downstream ENSMUSE00000324100 Chr11:106914103..106914328 GAGCGCTCTCTTTCTCAGGA Chr11:106914111..106914130 59.97 55
downstream ENSMUSE00000671062 Chr11:106914103..106914328 GAGCGCTCTCTTTCTCAGGA Chr11:106914111..106914130 59.97 55
downstream ENSMUSE00000324091 Chr11:106908314..106908657 CATCGTACGGTGTCTTGCAG Chr11:106908299..106908318 60.32 55
downstream ENSMUSE00000671061 Chr11:106908314..106908657 CATCGTACGGTGTCTTGCAG Chr11:106908299..106908318 60.32 55
downstream ENSMUSE00000324085 Chr11:106904947..106905139 CCCGTGGTACCAATTCTGAC Chr11:106905075..106905094 60.23 55
downstream ENSMUSE00000671059 Chr11:106904947..106905139 CCCGTGGTACCAATTCTGAC Chr11:106905075..106905094 60.23 55
downstream ENSMUSE00000324075 Chr11:106903989..106904073 GGTGCATCATTGGGGTCTAC Chr11:106903999..106904018 60.2 55
downstream ENSMUSE00000671058 Chr11:106903989..106904073 GGTGCATCATTGGGGTCTAC Chr11:106903999..106904018 60.2 55
downstream ENSMUSE00000324067 Chr11:106901540..106901726 TGGTCATATCTGCCACGAAC Chr11:106901630..106901649 59.53 50
downstream ENSMUSE00000671056 Chr11:106901540..106901726 TGGTCATATCTGCCACGAAC Chr11:106901630..106901649 59.53 50
downstream ENSMUSE00000576190 Chr11:106896860..106897153 CTTTTCCTTTGTCCGTTGGA Chr11:106896917..106896936 60.08 45
downstream ENSMUSE00000671040 Chr11:106894397..106897153 AAAAGCCTTACCGCCGTTAT Chr11:106894584..106894603 59.99 45
downstream ENSMUSE00000671069 Chr11:106894397..106897153 AAAAGCCTTACCGCCGTTAT Chr11:106894584..106894603 59.99 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCAGGCCTTTTCCTTTCTTT Chr11:106974585..106974605 59.7 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCAGGCCTTTTCCTTTCTTT Chr11:106974585..106974605 59.7 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AGTAATCGCCTTGCAGCACA Chr11:106975373..106975393 61.9 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GGTAGTTTTGTTTTGCTGTTTGG Chr11:106975434..106975457 59.96 39.13 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040481