Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI11609
Trapped Gene
Ubxn4 (ENSMUSG00000026353)
Vector Insertion
Chr 1: 130162992 - 130166445
Public Clones E139C01 (ggtc) P025A09 (ggtc) PST9654-NL (escells) IST10260D8 (tigm)
Private Clones OST39555 (lexicon) OST25133 (lexicon)
Severity of mutation (?) Insertion after 62% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000318758 (Chr1:130162867..130162991 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCAGGAACGGAAGTCAAGAG Chr1:130162948..130162967 59.99 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000318758 (Chr1:130162867..130162991 +)
Downstram Exon
ENSMUSE00000318754 (Chr1:130166446..130166548 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCAGGAACGGAAGTCAAGAG Chr1:130162948..130162967 59.99 55 CAGCCGGAACTGAATTCTTG Chr1:130166476..130166495 60.77 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000385394 Chr1:130140758..130141129 GTGACACAGGGGCGTACTTT Chr1:130140835..130140854 60.03 55
upstream ENSMUSE00000158291 Chr1:130148780..130148882 CTGCAAGTTGGGAAGATGAA Chr1:130148807..130148826 58.85 45
upstream ENSMUSE00000158290 Chr1:130152010..130152038 AAGCCTGTCTGCAGTTTTCAC Chr1:130152012..130152032 59.53 47.62
upstream ENSMUSE00000158286 Chr1:130152696..130152814 AATAGCGGGGAGTGTTTCTG Chr1:130152757..130152776 59.19 50
upstream ENSMUSE00000158284 Chr1:130155409..130155580 GTGAAAATCCCGAGTCCAAA Chr1:130155503..130155522 59.91 45
upstream ENSMUSE00000158288 Chr1:130156021..130156114 CACAGGTCATGACAGCCACT Chr1:130156031..130156050 59.74 55
upstream ENSMUSE00000158289 Chr1:130157411..130157465 GAGAAGCGGAAGGAAGAAGC Chr1:130157442..130157461 60.6 55
upstream ENSMUSE00000318763 Chr1:130159370..130159534 No primer for this exon
upstream ENSMUSE00000318758 Chr1:130162867..130162991 GCAGGAACGGAAGTCAAGAG Chr1:130162948..130162967 59.99 55

*** Putative Vector Insertion (Chr 1: 130162992 - 130166445) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000318754 Chr1:130166446..130166548 CAGCCGGAACTGAATTCTTG Chr1:130166476..130166495 60.77 50
downstream ENSMUSE00000318749 Chr1:130169398..130169529 GGGAAACATGGTGGCTAATG Chr1:130169448..130169467 60.19 50
downstream ENSMUSE00000318745 Chr1:130171379..130171581 GTGCAGGAGGAGGATTGCTA Chr1:130171517..130171536 60.36 55
downstream ENSMUSE00000338106 Chr1:130173534..130175954 GCTCGCTACCCTACATCTGC Chr1:130173685..130173704 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCATGGAGATAAGCACTTGACTAA Chr1:130162961..130162985 59.69 41.67 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TATGCATCTGGAACCGTGAC Chr1:130163029..130163049 59.53 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026353