Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI18529
Trapped Gene
Arid1b (ENSMUSG00000069729)
Vector Insertion
Chr 17: 5321478 - 5327275
Public Clones IST14955B7 (tigm)
Private Clones OST421309 (lexicon)
Severity of mutation (?) Insertion after 53% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000614504 (Chr17:5321273..5321477 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAACAAGAAGTGGCGTGAGC Chr17:5321281..5321300 60.44 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000614504 (Chr17:5321273..5321477 +)
Downstram Exon
ENSMUSE00000658486 (Chr17:5327276..5327414 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAACAAGAAGTGGCGTGAGC Chr17:5321281..5321300 60.44 50 GCTTTGCATGGGAGTCATCT Chr17:5327412..5327431 60.23 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000704213 Chr17:4994939..4996492 GCAGCAGCTAAACCAGTTCC Chr17:4995250..4995269 60.02 55
upstream ENSMUSE00000704207 Chr17:4996421..4996492 No primer for this exon
upstream ENSMUSE00000704206 Chr17:4996422..4996492 No primer for this exon
upstream ENSMUSE00000704212 Chr17:5040580..5040774 ATGGGTACTCACCCCCACTC Chr17:5040628..5040647 61.03 60
upstream ENSMUSE00000658488 Chr17:5097574..5097732 CAGCAAGCTGTGAGTGGCTA Chr17:5097592..5097611 60.35 55
upstream ENSMUSE00000707557 Chr17:5126914..5127024 CCTGGAAAATCCAACCATGA Chr17:5126962..5126981 60.69 45
upstream ENSMUSE00000614511 Chr17:5242828..5243071 AGTGCATCCGGGTCTACAAG Chr17:5242891..5242910 60.13 55
upstream ENSMUSE00000614510 Chr17:5264032..5264121 GGAAGCCAGTCAGAATCCAG Chr17:5264058..5264077 59.8 55
upstream ENSMUSE00000614509 Chr17:5279203..5279382 GCCCACAGATGAGCCAGTAT Chr17:5279353..5279372 60.1 55
upstream ENSMUSE00000704202 Chr17:5279215..5279382 TCTCAGTACGGACCTCAGCA Chr17:5279238..5279257 59.57 55
upstream ENSMUSE00000614508 Chr17:5290956..5291283 CAACCAGATGCATGGACAAG Chr17:5291041..5291060 60.11 50
upstream ENSMUSE00000577466 Chr17:5305749..5305894 CAACAACTCCAGCCTGATGA Chr17:5305821..5305840 59.83 50
upstream ENSMUSE00000614507 Chr17:5311835..5311944 GATGTCTCCCAGTGAGTCCAA Chr17:5311857..5311877 60.1 52.38
upstream ENSMUSE00000614506 Chr17:5313874..5314032 TATGGCTCTCAGGGCATTTC Chr17:5313880..5313899 60.18 50
upstream ENSMUSE00000614505 Chr17:5318641..5318850 TGTCTGCGTCAAGGAGATTG Chr17:5318817..5318836 59.98 50
upstream ENSMUSE00000614504 Chr17:5321273..5321477 AAACAAGAAGTGGCGTGAGC Chr17:5321281..5321300 60.44 50
upstream ENSMUSE00000704201 Chr17:5321273..5321476 AACCTGAACGTTGGCACTTC Chr17:5321309..5321328 60.16 50

*** Putative Vector Insertion (Chr 17: 5321478 - 5327275) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000658486 Chr17:5327276..5327414 GCTTTGCATGGGAGTCATCT Chr17:5327412..5327431 60.23 50
downstream ENSMUSE00000658485 Chr17:5327649..5327821 GCGTTTGGAGTCATGGAGTT Chr17:5327735..5327754 60.12 50
downstream ENSMUSE00000658484 Chr17:5332487..5332637 TGGTTCCATAGGGAAACTGC Chr17:5332627..5332646 59.93 50
downstream ENSMUSE00000658483 Chr17:5334964..5335060 CTGCTGTCCGTAAGCCTCAT Chr17:5334988..5335007 60.42 55
downstream ENSMUSE00000658482 Chr17:5336525..5337308 CGTGATTGATCCTCTGCTCA Chr17:5336942..5336961 59.94 50
downstream ENSMUSE00000658481 Chr17:5339216..5339346 CAGACCCGATTTAAGGGACA Chr17:5339265..5339284 59.93 50
downstream ENSMUSE00000658478 Chr17:5341363..5347656 AGCTCTCAGGGCAAACGATA Chr17:5346126..5346145 59.98 50
downstream ENSMUSE00000658480 Chr17:5341363..5343505 TGGGCAAGGTTCGATAAAAG Chr17:5342759..5342778 60.07 45
downstream ENSMUSE00000556742 Chr17:5341586..5343261 TGGGCAAGGTTCGATAAAAG Chr17:5342759..5342778 60.07 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCATCTCCTGGTAAGAGCA Chr17:5324468..5324488 60.36 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCATCTCCTGGTAAGAGCA Chr17:5324468..5324488 60.36 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000069729