Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI16523
Trapped Gene
Nfic (ENSMUSG00000055053)
Vector Insertion
Chr 10: 80863646 - 80863817
Public Clones not available
Private Clones OST459185 (lexicon) OST317055 (lexicon) OST288522 (lexicon)
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000705337 (Chr10:80863647..80863816 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCTGCATTTTTGGTGGAAAA Chr10:80863719..80863738 60.84 40 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000705337 (Chr10:80863647..80863816 -)
Downstram Exon
ENSMUSE00000383195 (Chr10:80863647..80863816 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCTGCATTTTTGGTGGAAAA Chr10:80863719..80863738 60.84 40 GGGGCTTCTCACTCCATCTA Chr10:80863676..80863695 59.24 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000708050 Chr10:80893531..80893750 No primer for this exon
upstream ENSMUSE00000665813 Chr10:80889821..80889902 GATGTATTCCTCCCCGCTCT Chr10:80889832..80889851 60.43 55
upstream ENSMUSE00000609202 Chr10:80883012..80883543 TGGACCTGTACCTGGCCTAC Chr10:80883028..80883047 59.99 60
upstream ENSMUSE00000609201 Chr10:80872356..80872427 CAGACCAGGAGGACAGCAAG Chr10:80872369..80872388 61 60
upstream ENSMUSE00000609200 Chr10:80871080..80871154 TGTCACGTCAGGTGTGTTCA Chr10:80871110..80871129 59.74 50
upstream ENSMUSE00000609206 Chr10:80870946..80870974 No primer for this exon
upstream ENSMUSE00000609199 Chr10:80870851..80870974 CCTGGCATATGACCTGAACC Chr10:80870900..80870919 60.34 55
upstream ENSMUSE00000609198 Chr10:80870300..80870424 CAACTCACCCACGAGTAGCA Chr10:80870330..80870349 59.9 55
upstream ENSMUSE00000609204 Chr10:80868835..80868959 CCAGCTTCACACAACACCAC Chr10:80868859..80868878 60.2 55
upstream ENSMUSE00000102220 Chr10:80868834..80868959 CCAGCTTCACACAACACCAC Chr10:80868859..80868878 60.2 55
upstream ENSMUSE00000491816 Chr10:80867569..80867753 TCCACCTACTTCCCCCATAC Chr10:80867663..80867682 58.72 55
upstream ENSMUSE00000495120 Chr10:80867569..80867715 TCCACCTACTTCCCCCATAC Chr10:80867663..80867682 58.72 55
upstream ENSMUSE00000609197 Chr10:80866097..80866173 CCTGCAAACAGTCCCTTTGT Chr10:80866131..80866150 60.15 50
upstream ENSMUSE00000721179 Chr10:80863698..80863816 GAGTCCCAGGGTGACAGTCC Chr10:80863742..80863761 61.96 65
upstream ENSMUSE00000383195 Chr10:80863647..80863816 CCTGCATTTTTGGTGGAAAA Chr10:80863719..80863738 60.84 40
upstream ENSMUSE00000705337 Chr10:80863647..80863816 CCTGCATTTTTGGTGGAAAA Chr10:80863719..80863738 60.84 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTTTCCTGACACCCAATTT Chr10:80863846..80863866 59.03 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATCACGTGACTGGGAAAACC Chr10:80863750..80863770 59.83 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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