Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI37800
Trapped Gene
Usp28 (ENSMUSG00000032267)
Vector Insertion
Chr 9: 48840794 - 48841681
Public Clones (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 68% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000369001 (Chr9:48840614..48840793 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCGCACCTAACTCTGAGGTC Chr9:48840705..48840724 59.87 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000369001 (Chr9:48840614..48840793 +)
Downstram Exon
ENSMUSE00000247286 (Chr9:48841682..48841777 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCGCACCTAACTCTGAGGTC Chr9:48840705..48840724 59.87 60 AAAGGTCTGGCGTGCTTTAG Chr9:48841747..48841766 59.52 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000479060 Chr9:48793490..48793642 GACAACGAGAGTGGGGCTAC Chr9:48793545..48793564 59.73 60
upstream ENSMUSE00000699592 Chr9:48808455..48808533 ATCAGCTGCGAGAAATCACA Chr9:48808475..48808494 59.55 45
upstream ENSMUSE00000478045 Chr9:48808456..48808533 ATCAGCTGCGAGAAATCACA Chr9:48808475..48808494 59.55 45
upstream ENSMUSE00000502520 Chr9:48809613..48809745 CCAGTCACGACACAACTGCT Chr9:48809674..48809693 59.94 55
upstream ENSMUSE00000699590 Chr9:48809613..48809745 CCAGTCACGACACAACTGCT Chr9:48809674..48809693 59.94 55
upstream ENSMUSE00000247372 Chr9:48811096..48811201 AGCCATTGCCTTGAGTCTCC Chr9:48811139..48811158 61.7 55
upstream ENSMUSE00000699589 Chr9:48811096..48811201 AGCCATTGCCTTGAGTCTCC Chr9:48811139..48811158 61.7 55
upstream ENSMUSE00000247816 Chr9:48811928..48812087 CCAGTTGGGCTGAAAAATGT Chr9:48812034..48812053 59.97 45
upstream ENSMUSE00000699587 Chr9:48811928..48812087 CCAGTTGGGCTGAAAAATGT Chr9:48812034..48812053 59.97 45
upstream ENSMUSE00000247793 Chr9:48816534..48816620 AACCTGCCACAGAACATCCT Chr9:48816579..48816598 59.58 50
upstream ENSMUSE00000699586 Chr9:48816534..48816620 AACCTGCCACAGAACATCCT Chr9:48816579..48816598 59.58 50
upstream ENSMUSE00000247768 Chr9:48817201..48817338 GCAGCCCTGGATCTACTGAA Chr9:48817288..48817307 60.36 55
upstream ENSMUSE00000699584 Chr9:48817201..48817338 GCAGCCCTGGATCTACTGAA Chr9:48817288..48817307 60.36 55
upstream ENSMUSE00000501591 Chr9:48818348..48818421 TCACACACAAGCTCCTGGAT Chr9:48818364..48818383 59.26 50
upstream ENSMUSE00000699583 Chr9:48818348..48818421 TCACACACAAGCTCCTGGAT Chr9:48818364..48818383 59.26 50
upstream ENSMUSE00000342673 Chr9:48819368..48819447 ATCCCATGGTGCAGCTATTC Chr9:48819394..48819413 59.92 50
upstream ENSMUSE00000699582 Chr9:48819368..48819447 ATCCCATGGTGCAGCTATTC Chr9:48819394..48819413 59.92 50
upstream ENSMUSE00000247710 Chr9:48823207..48823355 ACCTTCGGCCAGTATCCTCT Chr9:48823230..48823249 60.1 55
upstream ENSMUSE00000699580 Chr9:48823207..48823355 ACCTTCGGCCAGTATCCTCT Chr9:48823230..48823249 60.1 55
upstream ENSMUSE00000247685 Chr9:48824787..48824914 ACAAAGCTGCCTCCAGTGTT Chr9:48824796..48824815 59.91 50
upstream ENSMUSE00000247673 Chr9:48826477..48826572 AGAGAGCGTTCGGAAGTTGA Chr9:48826516..48826535 60.13 50
upstream ENSMUSE00000247649 Chr9:48832011..48832190 CCGATTTCTGACCTCACACC Chr9:48832162..48832181 60.51 55
upstream ENSMUSE00000247343 Chr9:48833873..48834093 CCTCGGACAGTCACAGATGA Chr9:48834009..48834028 59.82 55
upstream ENSMUSE00000247181 Chr9:48834924..48834994 GAAGGCGATTGAGCAGATGT Chr9:48834952..48834971 60.37 50
upstream ENSMUSE00000370627 Chr9:48836178..48836406 ATGACAACTTGCCCCACTTC Chr9:48836380..48836399 59.97 50
upstream ENSMUSE00000408618 Chr9:48838832..48839026 CTGGAGGTTTCAGCAAGAGG Chr9:48838917..48838936 59.98 55
upstream ENSMUSE00000247128 Chr9:48840319..48840458 GAGGTCCGATGCTTGTCTTC Chr9:48840342..48840361 59.81 55
upstream ENSMUSE00000369001 Chr9:48840614..48840793 CCGCACCTAACTCTGAGGTC Chr9:48840705..48840724 59.87 60

*** Putative Vector Insertion (Chr 9: 48840794 - 48841681) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000247286 Chr9:48841682..48841777 AAAGGTCTGGCGTGCTTTAG Chr9:48841747..48841766 59.52 50
downstream ENSMUSE00000247573 Chr9:48843698..48843876 CTACCCTCTTGGGTGCTTCA Chr9:48843824..48843843 60.25 55
downstream ENSMUSE00000247549 Chr9:48843987..48844065 TTCCATCAATTTGGCCTGAG Chr9:48844032..48844051 60.97 45
downstream ENSMUSE00000218240 Chr9:48845282..48845361 GGCCCGTTAGAAGGTACACA Chr9:48845342..48845361 59.99 55
downstream ENSMUSE00000218242 Chr9:48845873..48845996 TGCGGTATAAGGCAATCACA Chr9:48845985..48846004 60.1 45
downstream ENSMUSE00000218239 Chr9:48847087..48847282 GTCGTCCTTGGAGATGTCGT Chr9:48847224..48847243 60.12 55
downstream ENSMUSE00000350328 Chr9:48849479..48850622 CAGACACCCAATCCCTCTGT Chr9:48849760..48849779 59.96 55
downstream ENSMUSE00000699579 Chr9:48849479..48850615 CAGACACCCAATCCCTCTGT Chr9:48849760..48849779 59.96 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATGAGGAGGTACCGAGACGA Chr9:48840787..48840807 59.68 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATGAGGAGGTACCGAGACGA Chr9:48840787..48840807 59.68 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032267