Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI19075
Trapped Gene
Fank1 (ENSMUSG00000053111)
Vector Insertion
Chr 7: 141045027 - 141053785
Public Clones not available
Private Clones OST405401 (lexicon)
Severity of mutation (?) Insertion after 19% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000434184 (Chr7:141044849..141045026 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCACAGCTACGGTGTCATT Chr7:141045002..141045021 60.33 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000434184 (Chr7:141044849..141045026 +)
Downstram Exon
ENSMUSE00000434183 (Chr7:141053786..141053910 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCACAGCTACGGTGTCATT Chr7:141045002..141045021 60.33 50 ACCACATGCCTTGTTGCATA Chr7:141053812..141053831 59.99 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000434201 Chr7:140968544..140968653 AGACGAAGACAGGCGTTAGG Chr7:140968571..140968590 59.5 55
upstream ENSMUSE00000720162 Chr7:140968625..140968653 No primer for this exon
upstream ENSMUSE00000434184 Chr7:141044849..141045026 TGCACAGCTACGGTGTCATT Chr7:141045002..141045021 60.33 50

*** Putative Vector Insertion (Chr 7: 141045027 - 141053785) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000434183 Chr7:141053786..141053910 ACCACATGCCTTGTTGCATA Chr7:141053812..141053831 59.99 45
downstream ENSMUSE00000434178 Chr7:141059801..141059882 TCACACTGACAGCACGATGA Chr7:141059848..141059867 60.03 50
downstream ENSMUSE00000434175 Chr7:141060961..141061035 ATGAGAGCGGTAAAGCCAAA Chr7:141061011..141061030 59.85 45
downstream ENSMUSE00000434171 Chr7:141061705..141061770 GCCACTTCCGTTCTTCAGAT Chr7:141061765..141061784 59.29 50
downstream ENSMUSE00000434166 Chr7:141068431..141068596 CGTGTCTCCGGAGGTATTTG Chr7:141068492..141068511 60.51 55
downstream ENSMUSE00000434159 Chr7:141071562..141071705 GAGGCGTCTTTCCATCTTTG Chr7:141071703..141071722 59.81 50
downstream ENSMUSE00000434153 Chr7:141071955..141072032 CAGTTGCATCTGCCCCTTTA Chr7:141072024..141072043 61.16 50
downstream ENSMUSE00000434148 Chr7:141072127..141072171 TGGCCATTTCTAGGACACCT Chr7:141072157..141072176 59.55 50
downstream ENSMUSE00000434192 Chr7:141072281..141073206 TGGGAAGAGTTGCCCATTAC Chr7:141072500..141072519 59.93 50
downstream ENSMUSE00000711767 Chr7:141072281..141072548 CAGAGGACTTCCTTGGCATC Chr7:141072338..141072357 59.8 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCACAGCTACGGTGTCATT Chr7:141048003..141048023 60.33 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGCACAGCTACGGTGTCATT Chr7:141048003..141048023 60.33 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000053111