Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3994
Trapped Gene
Ccdc58 (ENSMUSG00000075229)
Vector Insertion
Chr 16: 36090047 - 36091919
Public Clones AR0336 (sanger) (sanger) D138D04 (ggtc) CMHD-GT_384C8-3 (cmhd) CMHD-GT_408B11-3 (cmhd)
CMHD-GT_446B4-3 (cmhd) CMHD-GT_397D1-3 (cmhd) (cmhd) FHCRC-GT-S17-11B1 (fhcrc)
Private Clones OST327921 (lexicon) OST315862 (lexicon) OST283730 (lexicon) OST248939 (lexicon)
OST237162 (lexicon) OST221819 (lexicon) OST217336 (lexicon) OST206451 (lexicon)
OST202584 (lexicon) OST109637 (lexicon) OST91751 (lexicon) OST52697 (lexicon)
OST32527 (lexicon)
Severity of mutation (?) Insertion after 89% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000644037 (Chr16:36089987..36090046 +)
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
ENSMUSE00000644037 (Chr16:36089987..36090046 +)
Downstram Exon
ENSMUSE00000644036 (Chr16:36091920..36092204 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon GCGATGAGATGACCGAGTCT Chr16:36092009..36092028 60.38 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000644041 Chr16:36072173..36072223 CTGTGAAGAGTTCGCCGAGT Chr16:36072199..36072218 60.59 55
upstream ENSMUSE00000644039 Chr16:36082777..36082902 TACGGTTCCAACAGCTTCCT Chr16:36082833..36082852 59.73 50
upstream ENSMUSE00000644038 Chr16:36085103..36085249 TGATGGCAGCTCATGTCAGT Chr16:36085104..36085123 60.44 50
upstream ENSMUSE00000644037 Chr16:36089987..36090046 No primer for this exon

*** Putative Vector Insertion (Chr 16: 36090047 - 36091919) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000644036 Chr16:36091920..36092204 GCGATGAGATGACCGAGTCT Chr16:36092009..36092028 60.38 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAGGAGCTGGAAGGTAGGAA Chr16:36090035..36090055 59.42 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGGAGCTGGAAGGTAGGAA Chr16:36090035..36090055 59.42 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000075229