Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29348
Trapped Gene
AC144621.3-201 (ENSMUSG00000024301)
Vector Insertion
Chr 17: 27058065 - 27058751
Public Clones PSTVU01.E2E (vanderbilt)
Private Clones not available
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000657976 (Chr17:27057965..27058064 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTGCAGTGACCAAAGTTGA Chr17:27057983..27058002 59.73 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000657976 (Chr17:27057965..27058064 +)
Downstram Exon
ENSMUSE00000503606 (Chr17:27058752..27058805 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTGCAGTGACCAAAGTTGA Chr17:27057983..27058002 59.73 50 CCACCAGGTCCTGTCTTCTT Chr17:27058788..27058807 59.15 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000610513 Chr17:27054036..27054230 CCTTTGCATCCCTTCCTGTG Chr17:27054184..27054203 62.87 55
upstream ENSMUSE00000449874 Chr17:27057742..27057876 GTCAAGTCCTCCTCCCGACT Chr17:27057790..27057809 60.65 60
upstream ENSMUSE00000657969 Chr17:27057850..27057876 No primer for this exon
upstream ENSMUSE00000657976 Chr17:27057965..27058064 GGTGCAGTGACCAAAGTTGA Chr17:27057983..27058002 59.73 50

*** Putative Vector Insertion (Chr 17: 27058065 - 27058751) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000503606 Chr17:27058752..27058805 CCACCAGGTCCTGTCTTCTT Chr17:27058788..27058807 59.15 55
downstream ENSMUSE00000657975 Chr17:27059621..27059668 No primer for this exon
downstream ENSMUSE00000450692 Chr17:27059850..27060094 CCAGCGTTTCAGTCTTCTCC Chr17:27059975..27059994 59.99 55
downstream ENSMUSE00000657974 Chr17:27059850..27060247 CCAGCGTTTCAGTCTTCTCC Chr17:27059975..27059994 59.99 55
downstream ENSMUSE00000478428 Chr17:27060160..27060213 CTCTCCCTGAAGCTCCTGAA Chr17:27060193..27060212 59.67 55
downstream ENSMUSE00000478480 Chr17:27060218..27060247 No primer for this exon
downstream ENSMUSE00000467416 Chr17:27060954..27061733 TAGCAGGTCTCGAACGGTCT Chr17:27061619..27061638 60.01 55
downstream ENSMUSE00000519682 Chr17:27062387..27062677 TGCTGTTAATGGCCTGTGTC Chr17:27062636..27062655 59.72 50
downstream ENSMUSE00000490427 Chr17:27062771..27062844 TGAGCTTGCTGTTTCGGTAA Chr17:27062807..27062826 59.61 45
downstream ENSMUSE00000474866 Chr17:27063165..27063240 TGGAAGCAAAGCGTAGTGAAT Chr17:27063240..27063260 59.9 42.86
downstream ENSMUSE00000701228 Chr17:27069049..27069524 AGGACCTGAAGCCCTGTTCT Chr17:27069355..27069374 60.25 55
downstream ENSMUSE00000707388 Chr17:27069049..27069093 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGACCAAGGGTGTGGAAGTG Chr17:27058086..27058106 60 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGACCAAGGGTGTGGAAGTG Chr17:27058086..27058106 60 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024301