Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1979
Trapped Gene
Ccdc12 (ENSMUSG00000019659)
Vector Insertion
Chr 9: 110559163 - 110594819
Public Clones AG0187 (sanger) AR0321 (sanger) (sanger) CC0253 (sanger) AQ0500 (sanger)
(sanger) RRT532 (baygenomics) RRT040 (baygenomics) D104C04 (ggtc)
(ggtc) (ggtc) D104C04 (ggtc) (ggtc) CMHD-GT_483D5-3 (cmhd) FHCRC-GT-S3-5B1 (fhcrc)
FHCRC-GT-S4-1B1 (fhcrc) (egtc) (egtc) IST14118D12 (tigm) IST13000A10 (tigm)
Private Clones OST425959 (lexicon) OST395701 (lexicon) OST395430 (lexicon) OST392421 (lexicon)
OST389942 (lexicon) OST381724 (lexicon) OST367871 (lexicon) OST366109 (lexicon)
OST338970 (lexicon) OST321571 (lexicon) OST270189 (lexicon) OST123570 (lexicon)
OST115805 (lexicon) OST85583 (lexicon) OST66624 (lexicon) OST56090 (lexicon)
OST1653 (lexicon)
Severity of mutation (?) Insertion after 19% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000220094 (Chr9:110559057..110559162 +)
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
ENSMUSE00000220094 (Chr9:110559057..110559162 +)
Downstram Exon
ENSMUSE00000305810 (Chr9:110594820..110594887 +)
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 ENSMUSE00000220094 Chr9:110559057..110559162 No primer for this exon

*** Putative Vector Insertion (Chr 9: 110559163 - 110594819) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000305810 Chr9:110594820..110594887 No primer for this exon
downstream ENSMUSE00000220088 Chr9:110610950..110611029 No primer for this exon
downstream ENSMUSE00000220093 Chr9:110612398..110612459 No primer for this exon
downstream ENSMUSE00000220091 Chr9:110612631..110612665 No primer for this exon
downstream ENSMUSE00000220089 Chr9:110613590..110613666 No primer for this exon
downstream ENSMUSE00000447808 Chr9:110613755..110614094 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGAGTGAGAGCTGCGGGTAT Chr9:110559176..110559196 61.72 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGGCACGGTGGAGTGAGAG Chr9:110592166..110592186 63.39 65 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000019659