Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8780
Trapped Gene
Cab39l (ENSMUSG00000021981)
Vector Insertion
Chr 14: 60078079 - 60080471
Public Clones Xk321 (baygenomics) F064F01 (ggtc)
Private Clones OST225404 (lexicon) OST50936 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000410236 (Chr14:60077923..60078078 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAGACTCCAGATTGGCGATT Chr14:60078016..60078035 60.22 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000410236 (Chr14:60077923..60078078 +)
Downstram Exon
ENSMUSE00000284089 (Chr14:60080472..60080539 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAGACTCCAGATTGGCGATT Chr14:60078016..60078035 60.22 50 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000335307 Chr14:60059823..60059848 No primer for this exon
upstream ENSMUSE00000410236 Chr14:60077923..60078078 CAGACTCCAGATTGGCGATT Chr14:60078016..60078035 60.22 50

*** Putative Vector Insertion (Chr 14: 60078079 - 60080471) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000284089 Chr14:60080472..60080539 No primer for this exon
downstream ENSMUSE00000339957 Chr14:60115640..60115781 AAATGGCCAGGTTGTCTTTC Chr14:60115755..60115774 59.03 45
downstream ENSMUSE00000706496 Chr14:60115671..60115781 CAAAATGGCCAGGTTGTCTT Chr14:60115757..60115776 59.97 45
downstream ENSMUSE00000122667 Chr14:60118381..60118545 GTCGTTCGTTCCACACAGAA Chr14:60118446..60118465 59.73 50
downstream ENSMUSE00000122665 Chr14:60125102..60125220 AGGACACCGTGTACCAATCTG Chr14:60125169..60125189 59.9 52.38
downstream ENSMUSE00000122670 Chr14:60138403..60138571 CAAAGGTGGACAGCTCAACA Chr14:60138542..60138561 59.87 50
downstream ENSMUSE00000122664 Chr14:60145593..60145652 No primer for this exon
downstream ENSMUSE00000284060 Chr14:60147679..60147744 TCAGATTGCAGCAGTTTCTCA Chr14:60147715..60147735 59.73 42.86
downstream ENSMUSE00000494461 Chr14:60157899..60158042 AGGCTTCGAATTGGATGTTG Chr14:60158031..60158050 60.07 45
downstream ENSMUSE00000376253 Chr14:60165823..60166187 AACTGCTCGTCGTCTGTCCT Chr14:60165944..60165963 60.06 55
downstream ENSMUSE00000687235 Chr14:60204341..60204397 CCATCTCTTCAGCCCATGTA Chr14:60204388..60204407 58.67 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCAAGGGCAGCATACTAAAA Chr14:60078050..60078071 60.75 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGCAAGGGCAGCATACTAAAA Chr14:60078050..60078071 60.75 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000021981