Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI32340
Trapped Gene
Fnbp1 (ENSMUSG00000075415)
Vector Insertion
Chr 2: 30961421 - 30965029
Public Clones (sanger) (sanger) IST14709D2 (tigm) IST14475H6 (tigm) IST10892C11 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 10% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000696128 (Chr2:30965016..30965028 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000696128 (Chr2:30965016..30965028 -)
Downstram Exon
ENSMUSE00000696142 (Chr2:30961422..30961429 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000479781 Chr2:30997299..30997526 CTTTCCGCATTCACAAGGTT Chr2:30997383..30997402 60.11 45
upstream ENSMUSE00000662797 Chr2:30997299..30997528 CTTTCCGCATTCACAAGGTT Chr2:30997383..30997402 60.11 45
upstream ENSMUSE00000696139 Chr2:30997299..30997322 No primer for this exon
upstream ENSMUSE00000696122 Chr2:30971745..30971807 ATGGAAGATGGCCTGATGAA Chr2:30971788..30971807 60.43 45
upstream ENSMUSE00000696128 Chr2:30965016..30965028 No primer for this exon
upstream ENSMUSE00000696143 Chr2:30965016..30965029 No primer for this exon
upstream ENSMUSE00000696142 Chr2:30961422..30961429 No primer for this exon

*** Putative Vector Insertion (Chr 2: 30961421 - 30965029) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000281967 Chr2:30960762..30960877 CCGTCCTCTCCTTGACAAAC Chr2:30960771..30960790 59.7 55
downstream ENSMUSE00000163540 Chr2:30952614..30952670 CCTCCTCTTCCTTCGAGTTCT Chr2:30952599..30952619 59.08 52.38
downstream ENSMUSE00000163542 Chr2:30951547..30951694 TCAGAGATGACCTCGTGCTG Chr2:30951595..30951614 60.14 55
downstream ENSMUSE00000163538 Chr2:30939543..30939605 CACGTTTCTATGTGCTGCTGA Chr2:30939540..30939560 60.06 47.62
downstream ENSMUSE00000163541 Chr2:30938494..30938598 CCTTACAGTCCCGCTCAAAC Chr2:30938546..30938565 59.73 55
downstream ENSMUSE00000717061 Chr2:30914409..30914537 TGGCGTATCTGAGCTTGTTG Chr2:30914490..30914509 60.01 50
downstream ENSMUSE00000722142 Chr2:30914409..30914537 TGGCGTATCTGAGCTTGTTG Chr2:30914490..30914509 60.01 50
downstream ENSMUSE00000696123 Chr2:30914128..30914133 No primer for this exon
downstream ENSMUSE00000281923 Chr2:30910948..30911094 CACCTCTGCGTACGTCTTCA Chr2:30911004..30911023 60.05 55
downstream ENSMUSE00000696119 Chr2:30910948..30911094 CACCTCTGCGTACGTCTTCA Chr2:30911004..30911023 60.05 55
downstream ENSMUSE00000568127 Chr2:30909544..30909738 GACACTGTGCGTTTCATTGG Chr2:30909619..30909638 60.16 50
downstream ENSMUSE00000696126 Chr2:30909511..30909738 GACACTGTGCGTTTCATTGG Chr2:30909619..30909638 60.16 50
downstream ENSMUSE00000662796 Chr2:30908755..30909738 TATCGATGCCACGGTACAAA Chr2:30908785..30908804 59.95 45
downstream ENSMUSE00000506828 Chr2:30908505..30908600 AGCAGTGGATTTTGGGTTTG Chr2:30908503..30908522 59.97 45
downstream ENSMUSE00000568126 Chr2:30908505..30908687 CTTTAGGCTCCGGAAGCAGT Chr2:30908489..30908508 60.88 55
downstream ENSMUSE00000696157 Chr2:30908505..30908657 AGCAGTGGATTTTGGGTTTG Chr2:30908503..30908522 59.97 45
downstream ENSMUSE00000696148 Chr2:30900402..30900416 No primer for this exon
downstream ENSMUSE00000604325 Chr2:30895925..30896034 CTCTGGTCCGTCTCCTTCTG Chr2:30895903..30895922 59.98 60
downstream ENSMUSE00000604324 Chr2:30892676..30892808 GGTGACTTCGGTGAGCTTCT Chr2:30892696..30892715 59.46 55
downstream ENSMUSE00000604323 Chr2:30892062..30892183 GTGACCGTCTGGTGTGTCTG Chr2:30892064..30892083 60.21 60
downstream ENSMUSE00000604322 Chr2:30891638..30891774 ATGTGTAGAGGGCCTTGCAG Chr2:30891622..30891641 60.28 55
downstream ENSMUSE00000568116 Chr2:30888550..30888708 CGTAGGAAGTGGGGACGTAA Chr2:30888558..30888577 59.99 55
downstream ENSMUSE00000696131 Chr2:30888530..30888708 CGTAGGAAGTGGGGACGTAA Chr2:30888558..30888577 59.99 55
downstream ENSMUSE00000335812 Chr2:30888523..30888708 CGTAGGAAGTGGGGACGTAA Chr2:30888558..30888577 59.99 55
downstream ENSMUSE00000696134 Chr2:30888519..30888708 CGTAGGAAGTGGGGACGTAA Chr2:30888558..30888577 59.99 55
downstream ENSMUSE00000696146 Chr2:30881727..30884403 GGAGAACAGGATCCGATGAA Chr2:30883457..30883476 60.01 50
downstream ENSMUSE00000696138 Chr2:30881726..30888708 AGCGGTAAATGTCACGTTCC Chr2:30882287..30882306 60 50
downstream ENSMUSE00000696149 Chr2:30881726..30884403 GGAGAACAGGATCCGATGAA Chr2:30883457..30883476 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGCAGAAACCCCTAGCCTCT Chr2:30961989..30962009 59.48 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGCAGAAACCCCTAGCCTCT Chr2:30961989..30962009 59.48 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000075415