Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5097
Trapped Gene
Ccdc76 (ENSMUSG00000033439)
Vector Insertion
Chr 3: 116288189 - 116288672
Public Clones CSG072 (baygenomics) YTC687 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 51% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000324497 (Chr3:116288673..116288745 -)
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
ENSMUSE00000324497 (Chr3:116288673..116288745 -)
Downstram Exon
ENSMUSE00000324490 (Chr3:116288114..116288188 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon CAGGTGCTTCCCAATTCCTA Chr3:116288108..116288127 60.07 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000443078 Chr3:116316677..116317505 GGTGGATATTCCGTTGATGG Chr3:116316880..116316899 60.01 50
upstream ENSMUSE00000401219 Chr3:116297557..116298511 AAAGGTTCTGTGGCGAACAC Chr3:116297572..116297591 60.16 50
upstream ENSMUSE00000324552 Chr3:116295382..116295428 No primer for this exon
upstream ENSMUSE00000324543 Chr3:116295111..116295177 No primer for this exon
upstream ENSMUSE00000324533 Chr3:116293148..116293210 TGCAGGATTAAAGGATGAAACA Chr3:116293166..116293187 59.59 36.36
upstream ENSMUSE00000324527 Chr3:116292652..116292721 No primer for this exon
upstream ENSMUSE00000324518 Chr3:116292409..116292515 GCATGATGCCCTTAATGACC Chr3:116292450..116292469 60.3 50
upstream ENSMUSE00000324508 Chr3:116291390..116291557 TGTTGAGTTTGGAGCAGGAA Chr3:116291482..116291501 59.42 45
upstream ENSMUSE00000324497 Chr3:116288673..116288745 No primer for this exon

*** Putative Vector Insertion (Chr 3: 116288189 - 116288672) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000324490 Chr3:116288114..116288188 CAGGTGCTTCCCAATTCCTA Chr3:116288108..116288127 60.07 50
downstream ENSMUSE00000324481 Chr3:116285412..116285841 CTCCATCATCGTGCTCTTCA Chr3:116285430..116285449 59.94 50
downstream ENSMUSE00000353072 Chr3:116284254..116284528 TGATGTTTTTCCTGCGATGA Chr3:116284315..116284334 60.2 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTCTAATCGCCTTGCAGCAC Chr3:116288604..116288624 61.07 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000033439