Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27548
Trapped Gene
Jazf1 (ENSMUSG00000063568)
Vector Insertion
Chr 6: 52762294 - 52843992
Public Clones IST11382E11 (tigm) IST14092B11 (tigm)
Private Clones OST57089 (lexicon)
Severity of mutation (?) Insertion after 26% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000498105 (Chr6:52843993..52844065 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTGGCCCTCAGTTACATCA Chr6:52843997..52844016 60.11 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000498105 (Chr6:52843993..52844065 -)
Downstram Exon
ENSMUSE00000373459 (Chr6:52762097..52762293 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTGGCCCTCAGTTACATCA Chr6:52843997..52844016 60.11 50 CACTGCTATGTCGAGGTGGA Chr6:52762144..52762163 59.85 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000561364 Chr6:53018447..53018589 CGATGTAGCACCATGACAGG Chr6:53018554..53018573 60.14 55
upstream ENSMUSE00000498105 Chr6:52843993..52844065 TGTGGCCCTCAGTTACATCA Chr6:52843997..52844016 60.11 50

*** Putative Vector Insertion (Chr 6: 52762294 - 52843992) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000373459 Chr6:52762097..52762293 CACTGCTATGTCGAGGTGGA Chr6:52762144..52762163 59.85 55
downstream ENSMUSE00000398052 Chr6:52727529..52727698 ACATGGAGCTGAGGATTGCT Chr6:52727572..52727591 59.83 50
downstream ENSMUSE00000616922 Chr6:52718791..52720374 GCGTATTAGGCAACCGGTAA Chr6:52718840..52718859 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCCCAGACTGAGGTTGTAGC Chr6:52765982..52766002 59.72 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCCCAGACTGAGGTTGTAGC Chr6:52765982..52766002 59.72 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AAGAACTGCTAATCGCCTTGC Chr6:52802003..52802024 60.88 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCTACATAAGAACTGCCGTGACT Chr6:52802008..52802031 59.72 47.83 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000063568