Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI21514
Trapped Gene
Ubxn4 (ENSMUSG00000026353)
Vector Insertion
Chr 1: 130141130 - 130148779
Public Clones not available
Private Clones OST327735 (lexicon) OST248751 (lexicon)
Severity of mutation (?) Insertion after 5% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000385394 (Chr1:130140758..130141129 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTGACACAGGGGCGTACTTT Chr1:130140835..130140854 60.03 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000385394 (Chr1:130140758..130141129 +)
Downstram Exon
ENSMUSE00000158291 (Chr1:130148780..130148882 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTGACACAGGGGCGTACTTT Chr1:130140835..130140854 60.03 55 CCAACTTGCAGCCATTTGTA Chr1:130148820..130148839 59.73 45

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

*** Putative Vector Insertion (Chr 1: 130141130 - 130148779) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000158291 Chr1:130148780..130148882 CCAACTTGCAGCCATTTGTA Chr1:130148820..130148839 59.73 45
downstream ENSMUSE00000158290 Chr1:130152010..130152038 No primer for this exon
downstream ENSMUSE00000158286 Chr1:130152696..130152814 TCCCCGCTATTACTTCCAAA Chr1:130152770..130152789 59.54 45
downstream ENSMUSE00000158284 Chr1:130155409..130155580 TTTGGACTCGGGATTTTCAC Chr1:130155525..130155544 59.91 45
downstream ENSMUSE00000158288 Chr1:130156021..130156114 AGTGGCTGTCATGACCTGTG Chr1:130156053..130156072 59.74 55
downstream ENSMUSE00000158289 Chr1:130157411..130157465 TCCTTCCGCTTCTCTTCTCTC Chr1:130157457..130157477 60.22 52.38
downstream ENSMUSE00000318763 Chr1:130159370..130159534 TCTCGAGCCGCTCTATCTTC Chr1:130159512..130159531 59.82 55
downstream ENSMUSE00000318758 Chr1:130162867..130162991 TGTCTTTGCAAAACGAGCAG Chr1:130162905..130162924 60.17 45
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 TCCTCACTTAATCGCCTTGC Chr1:130144173..130144193 60.35 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTGATTAACAAATATCGGAAAGC Chr1:130144119..130144143 58.68 29.17 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026353