Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8978
Trapped Gene
9030409G11Rik (ENSMUSG00000040606)
Vector Insertion
Chr 4: 141715096 - 141765929
Public Clones RRD004 (baygenomics) XD184 (baygenomics) RRE370 (baygenomics) PST3269-NL (escells)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000370854 (Chr4:141765930..141766121 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAGGACCTGGAGGAGTCACA Chr4:141766028..141766047 59.68 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000370854 (Chr4:141765930..141766121 -)
Downstram Exon
ENSMUSE00000596110 (Chr4:141714959..141715095 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAGGACCTGGAGGAGTCACA Chr4:141766028..141766047 59.68 55 CTGCTCATAGTTGCGGATGA Chr4:141714946..141714965 59.97 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000410441 Chr4:141794900..141795316 AAGCTATGCGCGGACACTAC Chr4:141794968..141794987 60.44 55
upstream ENSMUSE00000370854 Chr4:141765930..141766121 AAGGACCTGGAGGAGTCACA Chr4:141766028..141766047 59.68 55
upstream ENSMUSE00000524363 Chr4:141765930..141766127 AAGGACCTGGAGGAGTCACA Chr4:141766028..141766047 59.68 55

*** Putative Vector Insertion (Chr 4: 141715096 - 141765929) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000596110 Chr4:141714959..141715095 CTGCTCATAGTTGCGGATGA Chr4:141714946..141714965 59.97 50
downstream ENSMUSE00000596112 Chr4:141714959..141715095 CTGCTCATAGTTGCGGATGA Chr4:141714946..141714965 59.97 50
downstream ENSMUSE00000596109 Chr4:141710345..141710515 GTGCTTTGACTGCGTCTTCA Chr4:141710469..141710488 60.18 50
downstream ENSMUSE00000596111 Chr4:141710345..141710515 GTGCTTTGACTGCGTCTTCA Chr4:141710469..141710488 60.18 50
downstream ENSMUSE00000305891 Chr4:141706761..141706950 GGGAGGGTGTGAGTGGTAGA Chr4:141706758..141706777 59.96 60
downstream ENSMUSE00000411530 Chr4:141702933..141703060 GTCTTGGGGAGTTGATGTCG Chr4:141702934..141702953 60.51 55
downstream ENSMUSE00000305878 Chr4:141699209..141699259 AGGGTTGTGTAGGCTCTTCTGA Chr4:141699196..141699217 60.3 50
downstream ENSMUSE00000510231 Chr4:141697588..141697711 CTGGCGAAGACTCGAGAGAT Chr4:141697607..141697626 59.7 55
downstream ENSMUSE00000510247 Chr4:141695159..141697711 ACCTTACCCTGACGACGATG Chr4:141696853..141696872 59.99 55
downstream ENSMUSE00000454698 Chr4:141673990..141674195 TCTGCTCCTCTCCCTCAGAC Chr4:141674111..141674130 59.66 60
downstream ENSMUSE00000454690 Chr4:141673000..141673118 GCCTCAGCATCTCGGTAGTC Chr4:141672987..141673006 59.98 60
downstream ENSMUSE00000454683 Chr4:141668023..141668254 GTCCCGCTTCATCAGTGAAT Chr4:141668094..141668113 60.08 50
downstream ENSMUSE00000454676 Chr4:141665192..141665293 No primer for this exon
downstream ENSMUSE00000454670 Chr4:141664461..141664627 GACACCGCTATTGGTCAGGT Chr4:141664573..141664592 60 55
downstream ENSMUSE00000454661 Chr4:141662727..141662841 CCAGCTCTGGTGATGCTAGA Chr4:141662748..141662767 59.14 55
downstream ENSMUSE00000454654 Chr4:141658306..141660869 GGACTCAGGGAATCCTCCTC Chr4:141659251..141659270 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGCAGGAGTGAGCTGTTAGC Chr4:141759903..141759923 60.16 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGCAGGAGTGAGCTGTTAGC Chr4:141759903..141759923 60.16 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AGGCCAGGAAAGGTAAACTTC Chr4:141718149..141718170 58.77 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TTGTCCGATACTTTGTTGCAGTA Chr4:141718148..141718171 59.7 39.13 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040606