Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6338
Trapped Gene
Ptplad1 (ENSMUSG00000033629)
Vector Insertion
Chr 9: 64854442 - 64858280
Public Clones YHC292 (baygenomics)
Private Clones OST54882 (lexicon) OST36569 (lexicon)
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000250569 (Chr9:64858281..64858323 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCCTGCTATCAGCATCACAG Chr9:64858302..64858321 59.42 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000250569 (Chr9:64858281..64858323 -)
Downstram Exon
ENSMUSE00000250554 (Chr9:64854368..64854441 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCCTGCTATCAGCATCACAG Chr9:64858302..64858321 59.42 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000371131 Chr9:64869264..64869520 TGGAGACTCAAGTGCTGACG Chr9:64869330..64869349 60.18 55
upstream ENSMUSE00000250569 Chr9:64858281..64858323 CCCTGCTATCAGCATCACAG Chr9:64858302..64858321 59.42 55

*** Putative Vector Insertion (Chr 9: 64854442 - 64858280) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000250554 Chr9:64854368..64854441 No primer for this exon
downstream ENSMUSE00000250543 Chr9:64853415..64853579 CTCCATTTCCGCATCAGATT Chr9:64853405..64853424 60.04 45
downstream ENSMUSE00000250525 Chr9:64852064..64852115 No primer for this exon
downstream ENSMUSE00000250501 Chr9:64848788..64848898 CGCACTGTGAGGTTGACAAA Chr9:64848786..64848805 60.91 50
downstream ENSMUSE00000383853 Chr9:64846002..64846129 CAGCATTGAGGGTTTCCACT Chr9:64846024..64846043 60.11 50
downstream ENSMUSE00000350097 Chr9:64840064..64840176 AATTGCGCTCCAGGAATAAA Chr9:64840053..64840072 59.68 40
downstream ENSMUSE00000393131 Chr9:64838781..64838887 AGCACCTTCCAGTCCATGTC Chr9:64838818..64838837 60.12 55
downstream ENSMUSE00000358452 Chr9:64838124..64838255 CCTTCCCGACTCGTTGAATA Chr9:64838187..64838206 60.07 50
downstream ENSMUSE00000401613 Chr9:64834793..64836336 TGCGCAGTACTTCTCCCTTT Chr9:64835667..64835686 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTAATCGCCTTGCAGCACAT Chr9:64855210..64855230 61.32 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTTTGTACCGTGACTGGGAAA Chr9:64855216..64855237 59.88 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000033629