Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI247
Trapped Gene
Snf1lk (ENSMUSG00000024042)
Vector Insertion
Chr 17: 31987097 - 31987670
Public Clones GC0389 (tigem)
Private Clones not available
Severity of mutation (?) Insertion after 32% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000137472 (Chr17:31987671..31987794 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCTGTACGTCCTGGTCTGT Chr17:31987762..31987781 59.34 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000137472 (Chr17:31987671..31987794 -)
Downstram Exon
ENSMUSE00000137480 (Chr17:31986873..31987096 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCTGTACGTCCTGGTCTGT Chr17:31987762..31987781 59.34 55 CCCTAGCACCTGTTCGTTGT Chr17:31986893..31986912 60.17 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000490380 Chr17:31992617..31992737 No primer for this exon
upstream ENSMUSE00000314091 Chr17:31991839..31992009 GGTGATCATGTCGGAGTTCA Chr17:31991973..31991992 59.48 50
upstream ENSMUSE00000137475 Chr17:31991153..31991269 GGAGGTCCAGCTCATGAAAC Chr17:31991188..31991207 59.66 55
upstream ENSMUSE00000547826 Chr17:31988478..31988541 No primer for this exon
upstream ENSMUSE00000137478 Chr17:31988180..31988341 ACGGGCACTTGAGTGAAAAC Chr17:31988307..31988326 60.16 50
upstream ENSMUSE00000137474 Chr17:31987886..31988010 AAGTCTTCGAGGGGAAGGAG Chr17:31987913..31987932 59.81 55
upstream ENSMUSE00000137472 Chr17:31987671..31987794 TGCTGTACGTCCTGGTCTGT Chr17:31987762..31987781 59.34 55

*** Putative Vector Insertion (Chr 17: 31987097 - 31987670) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000137480 Chr17:31986873..31987096 CCCTAGCACCTGTTCGTTGT Chr17:31986893..31986912 60.17 55
downstream ENSMUSE00000137476 Chr17:31986464..31986619 AGGTAGTAAATGGCGGCAAA Chr17:31986551..31986570 59.61 45
downstream ENSMUSE00000137482 Chr17:31985904..31986026 AAAGGGTCACACGGGAGAAT Chr17:31985973..31985992 60.75 50
downstream ENSMUSE00000137484 Chr17:31985577..31985793 CTCGCTGATAGCTGTGTCCA Chr17:31985679..31985698 60.16 55
downstream ENSMUSE00000137487 Chr17:31984840..31985121 GAAGCTGACGGGAGGTAAGA Chr17:31984858..31984877 59.43 55
downstream ENSMUSE00000137485 Chr17:31983978..31984206 GTCCTCGCATTTTTCCTCAG Chr17:31984142..31984161 59.81 50
downstream ENSMUSE00000493746 Chr17:31981193..31983588 TACTGCTGCGGTGAGATTTG Chr17:31981941..31981960 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAGAGGTAATCGCCTTGCAG Chr17:31987605..31987625 59.48 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCATCCCCTTCTTCATGTCT Chr17:31987673..31987693 59.09 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024042