Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1457
Trapped Gene
Cnn3 (ENSMUSG00000053931)
Vector Insertion
Chr 3: 121129747 - 121152866
Public Clones XS0351 (sanger) (sanger) (sanger) CD0179 (sanger) (sanger)
CD0488 (sanger) (sanger) RRS022 (baygenomics) P140A03 (ggtc) D117A11 (ggtc)
H003E07 (ggtc) D117A11 (ggtc) H003E07 (ggtc) IST14428F5 (tigm) IST14262D7 (tigm)
IST11406G5 (tigm) IST10037C11 (tigm) IST14669A5 (tigm) IST15055D12 (tigm)
IST14965E5 (tigm) IST14584H4 (tigm)
Private Clones OST448804 (lexicon) OST415709 (lexicon) OST401902 (lexicon) OST396574 (lexicon)
OST282971 (lexicon) OST278196 (lexicon) OST273721 (lexicon) OST248295 (lexicon)
OST201904 (lexicon) OST188464 (lexicon) OST177463 (lexicon) OST175092 (lexicon)
OST168030 (lexicon) OST151676 (lexicon) OST129369 (lexicon) OST115700 (lexicon)
OST99691 (lexicon) OST45833 (lexicon) OST43124 (lexicon) OST35372 (lexicon)
OST34731 (lexicon)
Severity of mutation (?) Insertion after 6% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000359223 (Chr3:121129452..121129746 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGGGTGACTGACCGCTAGAA Chr3:121129647..121129666 59.87 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000359223 (Chr3:121129452..121129746 +)
Downstram Exon
ENSMUSE00000636208 (Chr3:121152867..121152988 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGGGTGACTGACCGCTAGAA Chr3:121129647..121129666 59.87 55 CAATATGATGCCGTCCTTCA Chr3:121152986..121153005 59.5 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000359223 Chr3:121129452..121129746 AGGGTGACTGACCGCTAGAA Chr3:121129647..121129666 59.87 55

*** Putative Vector Insertion (Chr 3: 121129747 - 121152866) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000636208 Chr3:121152867..121152988 CAATATGATGCCGTCCTTCA Chr3:121152986..121153005 59.5 45
downstream ENSMUSE00000636205 Chr3:121153210..121153276 GGGGCCAATTTAGTGAGGAT Chr3:121153277..121153296 60.15 50
downstream ENSMUSE00000463156 Chr3:121154301..121154438 CATGGGGCTTCATACCGTAA Chr3:121154361..121154380 60.71 50
downstream ENSMUSE00000465196 Chr3:121154801..121154917 CGCCAATGTCAATGGTTGTA Chr3:121154843..121154862 60.38 45
downstream ENSMUSE00000563954 Chr3:121157865..121158011 CAGGCTAATCGTGGTCTGGT Chr3:121157984..121158003 60.13 55
downstream ENSMUSE00000391013 Chr3:121160000..121160867 GTCTGGGTACTCGCCATGAT Chr3:121160296..121160315 59.96 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCTTTTCCCCAGTCTTCAT Chr3:121138710..121138730 60.44 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATACTCGTGACTGGGAAAACC Chr3:121138793..121138814 58.04 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000053931