Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI16442
Trapped Gene
Shf (ENSMUSG00000033256)
Vector Insertion
Chr 2: 122185326 - 122192419
Public Clones (sanger)
Private Clones OST461203 (lexicon) OST56196 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000446894 (Chr2:122192420..122192564 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAAAGCGAAGCCAGACAAG Chr2:122192420..122192439 60.13 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000446894 (Chr2:122192420..122192564 -)
Downstram Exon
ENSMUSE00000684300 (Chr2:122185184..122185325 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAAAGCGAAGCCAGACAAG Chr2:122192420..122192439 60.13 50 TGAGCCTTCACCAGTCTCCT Chr2:122185244..122185263 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000684301 Chr2:122194383..122194568 CGACTTCGAGGACCCCTACT Chr2:122194544..122194563 60.64 60
upstream ENSMUSE00000446894 Chr2:122192420..122192564 GAAAAGCGAAGCCAGACAAG Chr2:122192420..122192439 60.13 50

*** Putative Vector Insertion (Chr 2: 122185326 - 122192419) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000289917 Chr2:122185184..122185325 TGAGCCTTCACCAGTCTCCT Chr2:122185244..122185263 59.99 55
downstream ENSMUSE00000684300 Chr2:122185184..122185325 TGAGCCTTCACCAGTCTCCT Chr2:122185244..122185263 59.99 55
downstream ENSMUSE00000684291 Chr2:122183930..122183945 No primer for this exon
downstream ENSMUSE00000716804 Chr2:122183930..122183976 No primer for this exon
downstream ENSMUSE00000289910 Chr2:122182819..122183025 GGAAATCCGTTCCTTCTTCC Chr2:122182810..122182829 59.88 50
downstream ENSMUSE00000684298 Chr2:122181211..122181351 GGAGGCCAAGGTAGGTCTTT Chr2:122181293..122181312 59.58 55
downstream ENSMUSE00000715189 Chr2:122179767..122179933 TCTCCGATCCTTCAAACTGG Chr2:122179891..122179910 60.19 50
downstream ENSMUSE00000289904 Chr2:122179765..122179933 TCTCCGATCCTTCAAACTGG Chr2:122179891..122179910 60.19 50
downstream ENSMUSE00000289894 Chr2:122179501..122179620 TTTGCTGGTCTCACTGTTGC Chr2:122179502..122179521 60.03 50
downstream ENSMUSE00000721028 Chr2:122179501..122179620 TTTGCTGGTCTCACTGTTGC Chr2:122179502..122179521 60.03 50
downstream ENSMUSE00000714297 Chr2:122174935..122175275 TAGTGGTGCACGATTTCAGG Chr2:122175143..122175162 59.72 50
downstream ENSMUSE00000389234 Chr2:122174629..122175275 TAGTGGTGCACGATTTCAGG Chr2:122175143..122175162 59.72 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCTAGGCTTCAGTTGGGTGA Chr2:122192427..122192447 58.44 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTAGGCTTCAGTTGGGTGA Chr2:122189427..122189447 58.44 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TAATCGCCTTGCAGCACATC Chr2:122189494..122189514 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 AGCCACACAATCTGTGCTTTC Chr2:122192579..122192600 60.31 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000033256