Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI23386
Trapped Gene
Ccdc66 (ENSMUSG00000046753)
Vector Insertion
Chr 14: 28319902 - 28321607
Public Clones IST14495H6 (tigm) IST14778D9 (tigm)
Private Clones OST261477 (lexicon) OST96078 (lexicon)
Severity of mutation (?) Insertion after 1% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000486388 (Chr14:28321608..28321646 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000486388 (Chr14:28321608..28321646 -)
Downstram Exon
ENSMUSE00000375970 (Chr14:28319837..28319901 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000486388 Chr14:28321608..28321646 No primer for this exon

*** Putative Vector Insertion (Chr 14: 28319902 - 28321607) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000375970 Chr14:28319837..28319901 No primer for this exon
downstream ENSMUSE00000335585 Chr14:28318824..28318849 No primer for this exon
downstream ENSMUSE00000360786 Chr14:28313427..28313868 AAACCGCTGTTCATGGTCTC Chr14:28313506..28313525 60.12 50
downstream ENSMUSE00000351706 Chr14:28311910..28312075 CATTCACATCCTTTGGCTGA Chr14:28312000..28312019 59.65 45
downstream ENSMUSE00000460896 Chr14:28311627..28311730 TGTCAGCTGGTTTCCATTCA Chr14:28311683..28311702 60.24 45
downstream ENSMUSE00000463928 Chr14:28310525..28310637 CAGATGGCTTCCAAGGGTTA Chr14:28310544..28310563 60.07 50
downstream ENSMUSE00000462912 Chr14:28307267..28307398 GGACTCCAGCAGTCTTGCTT Chr14:28307356..28307375 59.6 55
downstream ENSMUSE00000465970 Chr14:28306458..28306708 TGTTTTCGGACCGTGTGATA Chr14:28306438..28306457 59.96 45
downstream ENSMUSE00000410901 Chr14:28306205..28306289 CTCCTCAATCTGGGCTGGAT Chr14:28306219..28306238 61.53 55
downstream ENSMUSE00000376883 Chr14:28304974..28305135 ACCTGAGCCATGATTGCTTT Chr14:28305094..28305113 59.7 45
downstream ENSMUSE00000331432 Chr14:28303849..28303993 TGTCCCTTCTGAGCCAGTTC Chr14:28303859..28303878 60.39 55
downstream ENSMUSE00000390035 Chr14:28303220..28303330 CTTCTTGGGAGAGGCTGTTG Chr14:28303217..28303236 59.98 55
downstream ENSMUSE00000518160 Chr14:28299790..28300136 TGGTAGCGCATCATTGAAAA Chr14:28300077..28300096 60.22 40
downstream ENSMUSE00000521136 Chr14:28299680..28299787 CTCGGGATTGTTTCTCTCCA Chr14:28299714..28299733 60.19 50
downstream ENSMUSE00000691071 Chr14:28299649..28300136 AGCGCATCATTGAAAATTCC Chr14:28300081..28300100 60.04 40
downstream ENSMUSE00000619215 Chr14:28298279..28298319 No primer for this exon
downstream ENSMUSE00000619214 Chr14:28297251..28297504 CTGGGTTGAAGGCCTAGACA Chr14:28297254..28297273 60.25 55
downstream ENSMUSE00000619213 Chr14:28296994..28297118 GCCCCTTAAGGATAGCTTGC Chr14:28296989..28297008 60.19 55
downstream ENSMUSE00000619212 Chr14:28295598..28295788 AAAATGCTGTTGCGTGGTAA Chr14:28295654..28295673 59.23 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTCGCTGGGCTGTAACTTTC Chr14:28321571..28321591 60.01 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTCGCTGGGCTGTAACTTTC Chr14:28321571..28321591 60.01 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GCATAGCGTTTGTTGAGCAG Chr14:28321674..28321694 59.64 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GCATAGCGTTTGTTGAGCAG Chr14:28321674..28321694 59.64 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000046753