Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6213
Trapped Gene
Azi2 (ENSMUSG00000039285)
Vector Insertion
Chr 9: 117958554 - 117959014
Public Clones CSG297 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 28% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000327094 (Chr9:117958428..117958553 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCATATCGTGAGGTTTGCATT Chr9:117958497..117958517 59.98 42.86 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000327094 (Chr9:117958428..117958553 +)
Downstram Exon
ENSMUSE00000327081 (Chr9:117959015..117959114 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCATATCGTGAGGTTTGCATT Chr9:117958497..117958517 59.98 42.86 TGCTGAGTCTCCACCTCTGTT Chr9:117959114..117959134 60.04 52.38

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000633738 Chr9:117949617..117950076 CCTACGTAGCCAGGGTTCAG Chr9:117950056..117950075 59.75 60
upstream ENSMUSE00000364911 Chr9:117956531..117956751 GCGTACCCTGGAGATGAGTC Chr9:117956617..117956636 59.69 60
upstream ENSMUSE00000327094 Chr9:117958428..117958553 GCATATCGTGAGGTTTGCATT Chr9:117958497..117958517 59.98 42.86

*** Putative Vector Insertion (Chr 9: 117958554 - 117959014) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000327081 Chr9:117959015..117959114 TGCTGAGTCTCCACCTCTGTT Chr9:117959114..117959134 60.04 52.38
downstream ENSMUSE00000327068 Chr9:117960472..117960620 GAGGTCACTGCACTCCTTCC Chr9:117960593..117960612 59.84 60
downstream ENSMUSE00000327057 Chr9:117964934..117965028 CTCGGCCTGATGACATCTCT Chr9:117964986..117965005 60.37 55
downstream ENSMUSE00000633732 Chr9:117968175..117968293 CTGCTTGCACTTGAGTCACC Chr9:117968254..117968273 59.62 55
downstream ENSMUSE00000382301 Chr9:117970832..117973025 GAGAACTGCACAAGCCATCA Chr9:117971347..117971366 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATCGCCTTGCAGCACATC Chr9:117958605..117958625 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTAGCACGTGACTGGGAAA Chr9:117958598..117958618 59.44 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039285