Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3352
Trapped Gene
Mcph1 (ENSMUSG00000039842)
Vector Insertion
Chr 8: 18595636 - 18596922
Public Clones XR0638 (sanger) IST11543D4 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000374723 (Chr8:18595173..18595635 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGCTGTCGTGTGTCACTGAG Chr8:18595413..18595432 60.53 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000374723 (Chr8:18595173..18595635 +)
Downstram Exon
ENSMUSE00000367954 (Chr8:18596923..18597014 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGCTGTCGTGTGTCACTGAG Chr8:18595413..18595432 60.53 60 GTTGCTTTGCAAACGTCCTT Chr8:18596997..18597016 60.29 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000374723 Chr8:18595173..18595635 GGCTGTCGTGTGTCACTGAG Chr8:18595413..18595432 60.53 60

*** Putative Vector Insertion (Chr 8: 18595636 - 18596922) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000367954 Chr8:18596923..18597014 GTTGCTTTGCAAACGTCCTT Chr8:18596997..18597016 60.29 45
downstream ENSMUSE00000361861 Chr8:18607279..18607397 TCACATGGGTCACTTGCTTG Chr8:18607318..18607337 60.72 50
downstream ENSMUSE00000408228 Chr8:18622607..18622694 CTGCAGGGAACAAAGACTCA Chr8:18622656..18622675 59.01 50
downstream ENSMUSE00000434141 Chr8:18625560..18625674 CTGCCTTTTGCCTTTGTAGC Chr8:18625671..18625690 60.02 50
downstream ENSMUSE00000226129 Chr8:18627118..18627240 CAGGAGGACAGGAACGTCAT Chr8:18627143..18627162 60.11 55
downstream ENSMUSE00000226124 Chr8:18629546..18629635 TTCTGCTGAGACTGCTCCAA Chr8:18629579..18629598 59.85 50
downstream ENSMUSE00000226116 Chr8:18631516..18632643 AAGAAGCCTCAACGTCAGGA Chr8:18632052..18632071 59.99 50
downstream ENSMUSE00000226106 Chr8:18641565..18641665 CCTGTGCAAGAGCTGTCTGA Chr8:18641619..18641638 60.33 55
downstream ENSMUSE00000226097 Chr8:18668946..18668983 No primer for this exon
downstream ENSMUSE00000226089 Chr8:18671092..18671254 ACCTGGATGATGAGGGTCTG Chr8:18671118..18671137 59.92 55
downstream ENSMUSE00000226081 Chr8:18688982..18689059 AATCCAGTGGCCCAACTCTA Chr8:18689017..18689036 59.55 50
downstream ENSMUSE00000434172 Chr8:18788239..18788476 TCGGCTGATTAGCAAAGAGG Chr8:18788308..18788327 60.48 50
downstream ENSMUSE00000332013 Chr8:18801406..18803186 ACTGGGGACACCAACAAGAG Chr8:18802460..18802479 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTAATCGCCTTGCAGCACAT Chr8:18595686..18595706 61.2 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTGAGGAGACACGCCCAGTA Chr8:18595637..18595657 61.28 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039842