Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI33754
Trapped Gene
Birc3 (ENSMUSG00000032000)
Vector Insertion
Chr 9: 7850919 - 7854607
Public Clones IST13439H2 (tigm) IST12334B6 (tigm) IST12334B6 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 73% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000301943 (Chr9:7854367..7854606 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGTGAGACAGACGGTTCAG Chr9:7854491..7854510 59.86 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000301943 (Chr9:7854367..7854606 -)
Downstram Exon
ENSMUSE00000215608 (Chr9:7850920..7851171 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGTGAGACAGACGGTTCAG Chr9:7854491..7854510 59.86 55 GGAGGCAATACAGCATTGGT Chr9:7851069..7851088 59.96 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000703788 Chr9:7872990..7873127 CAGGAAGTCACGCACAGAAG Chr9:7873092..7873111 59.62 55
upstream ENSMUSE00000215594 Chr9:7872823..7873024 AGCTGGGGACGATTTAAAGG Chr9:7872922..7872941 60.44 50
upstream ENSMUSE00000703786 Chr9:7872823..7872983 AGCTGGGGACGATTTAAAGG Chr9:7872922..7872941 60.44 50
upstream ENSMUSE00000215604 Chr9:7860463..7861407 GATAGAGTGGCCTGCTTTGC Chr9:7860696..7860715 59.99 55
upstream ENSMUSE00000714108 Chr9:7860463..7861407 GATAGAGTGGCCTGCTTTGC Chr9:7860696..7860715 59.99 55
upstream ENSMUSE00000215609 Chr9:7860263..7860362 GAACATGCCAAGTGGTTTCC Chr9:7860266..7860285 60.36 50
upstream ENSMUSE00000215615 Chr9:7858701..7858779 GCTCAGAATCAAAGGCCAAG Chr9:7858748..7858767 59.96 50
upstream ENSMUSE00000215595 Chr9:7857390..7857438 TCCCCAGAAGATGAGAATGC Chr9:7857401..7857420 60.16 50
upstream ENSMUSE00000703785 Chr9:7855815..7857438 ATGCAGACGCAGCAAGTATG Chr9:7857385..7857404 60.04 50
upstream ENSMUSE00000703787 Chr9:7854409..7854606 TGGTGAGACAGACGGTTCAG Chr9:7854491..7854510 59.86 55
upstream ENSMUSE00000301943 Chr9:7854367..7854606 TGGTGAGACAGACGGTTCAG Chr9:7854491..7854510 59.86 55
upstream ENSMUSE00000215608 Chr9:7850920..7851171 ACGTGTGTGACACCAATGCT Chr9:7851102..7851121 60.08 50

*** Putative Vector Insertion (Chr 9: 7850919 - 7854607) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000215611 Chr9:7849672..7849713 No primer for this exon
downstream ENSMUSE00000347462 Chr9:7848707..7849456 GATGGATACCTCTCGGTCCA Chr9:7849355..7849374 59.89 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTGGAGAAAGTTCGGAAGA Chr9:7854571..7854591 59.4 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTGGAGAAAGTTCGGAAGA Chr9:7854571..7854591 59.4 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032000