Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI21437
Trapped Gene
Usp28 (ENSMUSG00000032267)
Vector Insertion
Chr 9: 48826573 - 48832010
Public Clones IST13175A2 (tigm) IST13490B10 (tigm) IST13085B6 (tigm) IST13361B7 (tigm)
IST13316A3 (tigm) IST13168B7 (tigm) IST13084A6 (tigm) IST13085B6 (tigm)
IST13410B3 (tigm)
Private Clones OST330055 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000247673 (Chr9:48826477..48826572 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGAGAGCGTTCGGAAGTTGA Chr9:48826516..48826535 60.13 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000247673 (Chr9:48826477..48826572 +)
Downstram Exon
ENSMUSE00000247649 (Chr9:48832011..48832190 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGAGAGCGTTCGGAAGTTGA Chr9:48826516..48826535 60.13 50 CACCGAGGGAAGTGGTAATG Chr9:48832158..48832177 60.37 55

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

*** Putative Vector Insertion (Chr 9: 48826573 - 48832010) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000247649 Chr9:48832011..48832190 CACCGAGGGAAGTGGTAATG Chr9:48832158..48832177 60.37 55
downstream ENSMUSE00000247343 Chr9:48833873..48834093 CTGGGAAGAGCATCTTCTGG Chr9:48833944..48833963 59.94 55
downstream ENSMUSE00000247181 Chr9:48834924..48834994 TCGTGCTGCTCGAGATACAG Chr9:48834956..48834975 60.31 55
downstream ENSMUSE00000370627 Chr9:48836178..48836406 GAAGTGGGGCAAGTTGTCAT Chr9:48836402..48836421 59.97 50
downstream ENSMUSE00000408618 Chr9:48838832..48839026 CCTCTTGCTGAAACCTCCAG Chr9:48838939..48838958 59.98 55
downstream ENSMUSE00000247128 Chr9:48840319..48840458 GAAGACAAGCATCGGACCTC Chr9:48840364..48840383 59.81 55
downstream ENSMUSE00000369001 Chr9:48840614..48840793 TTCTTGGGCTCAGCTTCATT Chr9:48840639..48840658 59.96 45
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 AAGTAATCGCCTTGCAGCAC Chr9:48826621..48826641 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAAGCGTGACTGGGAAAACC Chr9:48829620..48829640 60.11 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032267