Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8712
Trapped Gene
Upf1 (ENSMUSG00000058301)
Vector Insertion
Chr 8: 72861532 - 72862104
Public Clones XN217 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 55% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000479641 (Chr8:72862105..72862219 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TAAGCGCACAGCTGAGAGAG Chr8:72862116..72862135 59.64 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000479641 (Chr8:72862105..72862219 -)
Downstram Exon
ENSMUSE00000484172 (Chr8:72861388..72861531 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TAAGCGCACAGCTGAGAGAG Chr8:72862116..72862135 59.64 55 CCAAGGACTACAGGCACCAT Chr8:72861376..72861395 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000508308 Chr8:72876677..72877178 CGAGTTCGAATTCACCGACT Chr8:72876781..72876800 60.26 50
upstream ENSMUSE00000507067 Chr8:72868125..72868264 ATGACAGTGTGGCCAAGACC Chr8:72868208..72868227 61 55
upstream ENSMUSE00000503574 Chr8:72867234..72867323 CTGCCTGCGTGGTTTACTGT Chr8:72867284..72867303 61.28 55
upstream ENSMUSE00000510662 Chr8:72865909..72866076 AGACCGTGCTGGAGTGCTAC Chr8:72865986..72866005 60.48 60
upstream ENSMUSE00000507971 Chr8:72865359..72865539 TTCTGTCATGGCTGGTCAAG Chr8:72865437..72865456 59.83 50
upstream ENSMUSE00000517434 Chr8:72864449..72864610 GCGTTACGAGGATGCTTACC Chr8:72864520..72864539 59.74 55
upstream ENSMUSE00000514355 Chr8:72863881..72863998 AATCGCCTTCTTCACTTTGC Chr8:72863929..72863948 59.46 45
upstream ENSMUSE00000511605 Chr8:72863642..72863740 GATCTGTCTGCGGTACAAAGG Chr8:72863695..72863715 59.75 52.38
upstream ENSMUSE00000516593 Chr8:72863223..72863331 TGTGGAAGTGACCCACAACT Chr8:72863263..72863282 58.99 50
upstream ENSMUSE00000480446 Chr8:72862979..72863138 TCCCTGACCTCAACCACTCT Chr8:72862982..72863001 59.68 55
upstream ENSMUSE00000485136 Chr8:72862785..72862903 GAGACCACTCAGCCTCATCC Chr8:72862858..72862877 59.8 60
upstream ENSMUSE00000482604 Chr8:72862296..72862460 TTGCACAACCAGATCAGGAA Chr8:72862305..72862324 60.24 45
upstream ENSMUSE00000479641 Chr8:72862105..72862219 TAAGCGCACAGCTGAGAGAG Chr8:72862116..72862135 59.64 55

*** Putative Vector Insertion (Chr 8: 72861532 - 72862104) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000484172 Chr8:72861388..72861531 CCAAGGACTACAGGCACCAT Chr8:72861376..72861395 59.99 55
downstream ENSMUSE00000490629 Chr8:72860916..72861129 GCAATGAGCCCTCGTAGAAG Chr8:72860912..72860931 59.98 55
downstream ENSMUSE00000486077 Chr8:72859553..72859670 GTGGCCACTGGAAGTCAAAG Chr8:72859610..72859629 60.69 55
downstream ENSMUSE00000483169 Chr8:72859132..72859288 TGCCTTCAACAGCTTCGTAGT Chr8:72859218..72859238 60.07 47.62
downstream ENSMUSE00000493592 Chr8:72858517..72858659 GGGTCGTTTAGGAACCCAAT Chr8:72858528..72858547 60.05 50
downstream ENSMUSE00000494397 Chr8:72857972..72858146 TTCCACTAGCGCCTTCTGTT Chr8:72858025..72858044 60.01 50
downstream ENSMUSE00000487755 Chr8:72857792..72857873 GGCATCGTACATGGCAGTAG Chr8:72857816..72857835 59.18 55
downstream ENSMUSE00000488514 Chr8:72857170..72857331 CTGTCCGAAGTAGCCAGGTG Chr8:72857167..72857186 60.84 60
downstream ENSMUSE00000497214 Chr8:72856872..72857089 CATGGACACGTAACCCTGTG Chr8:72856904..72856923 59.87 55
downstream ENSMUSE00000498109 Chr8:72856519..72856641 GAGTGCCACGTCAATCTGTG Chr8:72856572..72856591 60.32 55
downstream ENSMUSE00000491289 Chr8:72855432..72856378 GTGGCCTCTGAAGCTCAAAC Chr8:72855602..72855621 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAAGCGCACAGCTGAGAGAG Chr8:72862114..72862134 59.64 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAAGCGCACAGCTGAGAGAG Chr8:72862114..72862134 59.64 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000058301