Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI33704
Trapped Gene
Nfic (ENSMUSG00000055053)
Vector Insertion
Chr 10: 80863697 - 80866174
Public Clones IST13962E2 (tigm) IST14158G6 (tigm) IST13801H2 (tigm) IST13633A9 (tigm)
IST10318C2 (tigm) IST10318C2 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 99% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000609197 (Chr10:80866097..80866173 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCTGCAAACAGTCCCTTTGT Chr10:80866131..80866150 60.15 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000609197 (Chr10:80866097..80866173 -)
Downstram Exon
ENSMUSE00000721179 (Chr10:80863698..80863816 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCTGCAAACAGTCCCTTTGT Chr10:80866131..80866150 60.15 50 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

*** Putative Vector Insertion (Chr 10: 80863697 - 80866174) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000383195 Chr10:80863647..80863816 GGGGCTTCTCACTCCATCTA Chr10:80863676..80863695 59.24 55
downstream ENSMUSE00000705337 Chr10:80863647..80863816 GGGGCTTCTCACTCCATCTA Chr10:80863676..80863695 59.24 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGCAAACAGTCCCTTTGTG Chr10:80866128..80866148 59.33 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGATTCGTGACTGGGAAAAC Chr10:80866108..80866128 59.39 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000055053