Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5825
Trapped Gene
Zfp609 (ENSMUSG00000040524)
Vector Insertion
Chr 9: 65553986 - 65578782
Public Clones CSH682 (baygenomics) IST14407C5 (tigm) IST14407C5 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 20% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000421905 (Chr9:65578783..65579008 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGTACCCGATCAGTTGGTGT Chr9:65578890..65578909 60.83 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000421905 (Chr9:65578783..65579008 -)
Downstram Exon
ENSMUSE00000347915 (Chr9:65553898..65553985 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGTACCCGATCAGTTGGTGT Chr9:65578890..65578909 60.83 55 CAATCATGCCTTGTGCAGTC Chr9:65553888..65553907 60.27 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000421911 Chr9:65642429..65643134 ACCTCATCATCGACCTGGAC Chr9:65643059..65643078 59.93 55
upstream ENSMUSE00000696965 Chr9:65642429..65643175 ACCTCATCATCGACCTGGAC Chr9:65643059..65643078 59.93 55
upstream ENSMUSE00000421905 Chr9:65578783..65579008 CGTACCCGATCAGTTGGTGT Chr9:65578890..65578909 60.83 55

*** Putative Vector Insertion (Chr 9: 65553986 - 65578782) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000347915 Chr9:65553898..65553985 CAATCATGCCTTGTGCAGTC Chr9:65553888..65553907 60.27 50
downstream ENSMUSE00000388050 Chr9:65550079..65552425 GGCACGTAGGCATACTGGTT Chr9:65550526..65550545 60.02 55
downstream ENSMUSE00000246135 Chr9:65548629..65548995 TCTTTCCACCGATCATCCTC Chr9:65548894..65548913 60.01 50
downstream ENSMUSE00000246119 Chr9:65545301..65545476 GCCATACGGGGAGAAAGAAT Chr9:65545414..65545433 60.29 50
downstream ENSMUSE00000411360 Chr9:65544839..65545055 GCGGCATAGGGTAGGTTGTA Chr9:65544819..65544838 59.98 55
downstream ENSMUSE00000352537 Chr9:65543950..65544028 AGTGAGGGAGTTGAGCCTTG Chr9:65543955..65543974 59.45 55
downstream ENSMUSE00000584165 Chr9:65543269..65543501 TGACTTCATCTGGGCACTTG Chr9:65543455..65543474 59.83 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGTTGCAGTCGTCCTGCTTA Chr9:65569729..65569749 58.68 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGCTCGTGACTGGGAAAAC Chr9:65569716..65569736 60.83 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TCCCTGTCACATTGTTCCAA Chr9:65570023..65570043 59.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TCCCTGTCACATTGTTCCAA Chr9:65570023..65570043 59.94 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040524