Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6153
Trapped Gene
Hnrnpu (ENSMUSG00000039630)
Vector Insertion
Chr 1: 180266290 - 180267083
Public Clones YHC129 (baygenomics) CSG051 (baygenomics) D035B10 (ggtc) PST1265-2 (escells)
PST961-3 (escells) IST10852A7 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 26% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000591904 (Chr1:180267084..180267915 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGCCCTCAACATGAGTTCTT Chr1:180267693..180267712 59.14 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000591904 (Chr1:180267084..180267915 -)
Downstram Exon
ENSMUSE00000320768 (Chr1:180266178..180266289 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGCCCTCAACATGAGTTCTT Chr1:180267693..180267712 59.14 50 CTTCTCGCGGTCTTTTAACG Chr1:180266205..180266224 60.01 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000591904 Chr1:180267084..180267915 GGCCCTCAACATGAGTTCTT Chr1:180267693..180267712 59.14 50

*** Putative Vector Insertion (Chr 1: 180266290 - 180267083) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000320768 Chr1:180266178..180266289 CTTCTCGCGGTCTTTTAACG Chr1:180266205..180266224 60.01 50
downstream ENSMUSE00000320763 Chr1:180266013..180266086 No primer for this exon
downstream ENSMUSE00000320756 Chr1:180264018..180264157 TGCCTTTTGACACACCGTAG Chr1:180264016..180264035 59.76 50
downstream ENSMUSE00000320749 Chr1:180263678..180263777 AGCCAATCCGAACTTCATGT Chr1:180263686..180263705 59.56 45
downstream ENSMUSE00000320744 Chr1:180263128..180263240 No primer for this exon
downstream ENSMUSE00000320736 Chr1:180262224..180262487 CAACTGCACAGTTATGGCAGA Chr1:180262330..180262350 59.92 47.62
downstream ENSMUSE00000320726 Chr1:180261966..180262085 CCCAGGTAGTTTTTCCAGCTC Chr1:180262018..180262038 60.12 52.38
downstream ENSMUSE00000320719 Chr1:180261480..180261608 CTTCTTACGGGCAGCAATTT Chr1:180261479..180261498 59.36 45
downstream ENSMUSE00000320707 Chr1:180261224..180261392 TTTGGGCACACTACAACAGC Chr1:180261288..180261307 59.76 50
downstream ENSMUSE00000320702 Chr1:180260723..180260977 GCCACCACCTCTGTTGAACT Chr1:180260753..180260772 60.16 55
downstream ENSMUSE00000320695 Chr1:180260296..180260477 TAGCCAATTCCACCACTTCC Chr1:180260374..180260393 59.93 50
downstream ENSMUSE00000320688 Chr1:180259999..180260070 GCCACGATTATTTCCTCGTC Chr1:180260019..180260038 59.53 50
downstream ENSMUSE00000591898 Chr1:180258431..180259538 TGCACAATGCTGAGGTTCTC Chr1:180259241..180259260 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGAGGTAAGAAGGCGGAAGG Chr1:180267066..180267086 62.31 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGAGGTAAGAAGGCGGAAGG Chr1:180267066..180267086 62.31 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GTAATCGCCTTGCAGCACATC Chr1:180267845..180267866 62.97 52.38 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000039630