Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27307
Trapped Gene
Sfrs12 (ENSMUSG00000032621)
Vector Insertion
Chr 13: 104538935 - 104542473
Public Clones not available
Private Clones OST64126 (lexicon)
Severity of mutation (?) Insertion after 74% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000406921 (Chr13:104542474..104542782 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACAAGGAGCGGGGTAAAAAC Chr13:104542668..104542687 60.35 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000406921 (Chr13:104542474..104542782 -)
Downstram Exon
ENSMUSE00000314846 (Chr13:104538839..104538934 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACAAGGAGCGGGGTAAAAAC Chr13:104542668..104542687 60.35 50 TGGAAGAACTCCTGCTCCTC Chr13:104538878..104538897 59.53 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000679910 Chr13:104564379..104564539 CCTACGACGGTGATTCAGGT Chr13:104564472..104564491 59.99 55
upstream ENSMUSE00000679909 Chr13:104559397..104559530 TGTGGCCCAGCATCTAACTA Chr13:104559445..104559464 59.3 50
upstream ENSMUSE00000610802 Chr13:104553962..104554584 ATCCCAACCTCCAGTCCTCT Chr13:104553978..104553997 59.93 55
upstream ENSMUSE00000679908 Chr13:104553962..104554086 ATCCCAACCTCCAGTCCTCT Chr13:104553978..104553997 59.93 55
upstream ENSMUSE00000314908 Chr13:104551110..104551274 GCGCTGGACCCAAATATTAC Chr13:104551213..104551232 59.44 50
upstream ENSMUSE00000314898 Chr13:104550496..104550674 AACTCGGTTTGCTTTTGTGG Chr13:104550569..104550588 60.15 45
upstream ENSMUSE00000314888 Chr13:104549249..104549379 TCAGGCTGCAGCTAAGGAGT Chr13:104549312..104549331 60.3 55
upstream ENSMUSE00000314878 Chr13:104548266..104548380 GTCGATCTCGTTCCCACACT Chr13:104548331..104548350 60.12 55
upstream ENSMUSE00000314870 Chr13:104543105..104543224 AGTCTAGGGAGAGGCGGAAG Chr13:104543128..104543147 59.97 60
upstream ENSMUSE00000406921 Chr13:104542474..104542782 ACAAGGAGCGGGGTAAAAAC Chr13:104542668..104542687 60.35 50

*** Putative Vector Insertion (Chr 13: 104538935 - 104542473) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000314846 Chr13:104538839..104538934 TGGAAGAACTCCTGCTCCTC Chr13:104538878..104538897 59.53 55
downstream ENSMUSE00000314839 Chr13:104534865..104535009 CTGATGTGGTCCCGTTCTTT Chr13:104534940..104534959 59.97 50
downstream ENSMUSE00000438880 Chr13:104531695..104533796 CATTTTCTGGCAGACCCAAT Chr13:104532934..104532953 59.93 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTTGCAGTGATGCAAGAGGA Chr13:104542472..104542492 60.54 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTGCAGTGATGCAAGAGGA Chr13:104542472..104542492 60.54 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032621