Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3172
Trapped Gene
Dars (ENSMUSG00000026356)
Vector Insertion
Chr 1: 130266113 - 130268716
Public Clones XS0759 (sanger)
Private Clones OST198709 (lexicon)
Severity of mutation (?) Insertion after 74% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000158362 (Chr1:130268717..130268863 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGAGTTGAAATGGACGATG Chr1:130268730..130268749 59.5 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000158362 (Chr1:130268717..130268863 -)
Downstram Exon
ENSMUSE00000158357 (Chr1:130266070..130266112 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGAGTTGAAATGGACGATG Chr1:130268730..130268749 59.5 45 CCAAACGACCCAACAGTTTT Chr1:130266059..130266078 59.87 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000539985 Chr1:130313729..130313902 GGTATCCACTCCCCAAATCC Chr1:130313804..130313823 60.39 55
upstream ENSMUSE00000158352 Chr1:130311931..130311988 No primer for this exon
upstream ENSMUSE00000158349 Chr1:130310237..130310329 GGTCCGTGCAAGAGTTCATA Chr1:130310252..130310271 58.72 50
upstream ENSMUSE00000539984 Chr1:130308925..130308971 CCTACCGACCGTTTGTTCTT Chr1:130308944..130308963 59.1 50
upstream ENSMUSE00000158353 Chr1:130301943..130302045 TGCAAGCAAGCAGATGGTTA Chr1:130301956..130301975 60.54 45
upstream ENSMUSE00000158360 Chr1:130287848..130287950 TGTACCCAGCAGGATGTTGA Chr1:130287864..130287883 60.11 50
upstream ENSMUSE00000158363 Chr1:130285696..130285776 GATCAGCTTGGCTGAACCTC Chr1:130285749..130285768 59.96 55
upstream ENSMUSE00000158359 Chr1:130283694..130283753 No primer for this exon
upstream ENSMUSE00000158358 Chr1:130275343..130275454 TGCCATCTCTTCCGAGAAAC Chr1:130275393..130275412 60.34 50
upstream ENSMUSE00000158361 Chr1:130272755..130272889 TGAAGGAGGAGCCAATGTTT Chr1:130272863..130272882 59.67 45
upstream ENSMUSE00000158348 Chr1:130270514..130270661 TTGCTGACACTTTGGTGCAA Chr1:130270537..130270556 61.45 45
upstream ENSMUSE00000158362 Chr1:130268717..130268863 TGGAGTTGAAATGGACGATG Chr1:130268730..130268749 59.5 45

*** Putative Vector Insertion (Chr 1: 130266113 - 130268716) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000158357 Chr1:130266070..130266112 CCAAACGACCCAACAGTTTT Chr1:130266059..130266078 59.87 45
downstream ENSMUSE00000158354 Chr1:130264942..130265022 TGGGTCAGGCATGGTATAGA Chr1:130264929..130264948 58.95 50
downstream ENSMUSE00000158350 Chr1:130263498..130263609 CATGGATTCTTTGTGCTCCA Chr1:130263518..130263537 59.65 45
downstream ENSMUSE00000158356 Chr1:130263275..130263346 CAAAGCGGAAGGAATCAATG Chr1:130263283..130263302 60.58 45
downstream ENSMUSE00000343891 Chr1:130260285..130260902 GTGGCTTTAAGGCGTGAGTC Chr1:130260783..130260802 59.88 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATAATCGCCTTGCAGCACA Chr1:130268647..130268667 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGAAATGGACGATGAGGAA Chr1:130268723..130268743 59.05 40 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026356