Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4483
Trapped Gene
Ube2l3 (ENSMUSG00000038965)
Vector Insertion
Chr 16: 17160270 - 17176504
Public Clones XT0496 (sanger) CMHD-GT_424E11-3 (cmhd) IST14301H7 (tigm)
Private Clones OST452255 (lexicon) OST431143 (lexicon) OST428133 (lexicon) OST373681 (lexicon)
OST340420 (lexicon) OST339848 (lexicon) OST324178 (lexicon) OST310925 (lexicon)
OST296728 (lexicon) OST279536 (lexicon) OST277865 (lexicon) OST277116 (lexicon)
OST232481 (lexicon) OST231843 (lexicon) OST231474 (lexicon) OST227120 (lexicon)
OST217183 (lexicon) OST207923 (lexicon) OST176349 (lexicon) OST172026 (lexicon)
OST165059 (lexicon) OST149543 (lexicon) OST139744 (lexicon) OST138816 (lexicon)
OST136779 (lexicon) OST136016 (lexicon) OST135663 (lexicon) OST118731 (lexicon)
OST113645 (lexicon) OST96476 (lexicon) OST89606 (lexicon) OST59598 (lexicon)
OST52328 (lexicon) OST45166 (lexicon) OST38463 (lexicon) OST30776 (lexicon)
OST27565 (lexicon) OST26371 (lexicon) OST24340 (lexicon) OST23864 (lexicon)
OST23545 (lexicon) OST22356 (lexicon) OST22257 (lexicon) OST20922 (lexicon)
OST19920 (lexicon) OST18649 (lexicon) OST18362 (lexicon) OST17260 (lexicon)
OST17093 (lexicon) OST15832 (lexicon) OST14806 (lexicon) OST14761 (lexicon)
OST14434 (lexicon) OST14130 (lexicon) OST14119 (lexicon) OST13495 (lexicon)
OST12850 (lexicon) OST12328 (lexicon) OST9024 (lexicon) OST7076 (lexicon)
OST1754 (lexicon) OST946 (lexicon)
Severity of mutation (?) Insertion after 26% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000562491 (Chr16:17176505..17176600 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCTTGAAGAGATCCGCAAA Chr16:17176580..17176599 60.1 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000562491 (Chr16:17176505..17176600 -)
Downstram Exon
ENSMUSE00000520774 (Chr16:17160083..17160269 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCTTGAAGAGATCCGCAAA Chr16:17176580..17176599 60.1 45 TGTGATCTTGGGTGGTTTGA Chr16:17160164..17160183 59.94 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000703894 Chr16:17202589..17202742 CCTTTCTAATGGGCACATGG Chr16:17202609..17202628 60.32 50
upstream ENSMUSE00000645501 Chr16:17201528..17201563 No primer for this exon
upstream ENSMUSE00000703893 Chr16:17201528..17201726 TTCTCTATTCCGCGCTCTTC Chr16:17201650..17201669 59.69 50
upstream ENSMUSE00000703899 Chr16:17201528..17201587 AGCAGCACCAGATCCAAGAT Chr16:17201553..17201572 59.83 50
upstream ENSMUSE00000562491 Chr16:17176505..17176600 AGCTTGAAGAGATCCGCAAA Chr16:17176580..17176599 60.1 45

*** Putative Vector Insertion (Chr 16: 17160270 - 17176504) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000520774 Chr16:17160083..17160269 TGTGATCTTGGGTGGTTTGA Chr16:17160164..17160183 59.94 45
downstream ENSMUSE00000703898 Chr16:17154353..17154375 CAGTGCTATGAGGGACTGGA Chr16:17154331..17154350 58.83 55
downstream ENSMUSE00000629265 Chr16:17153418..17154375 TGGAAGTGGGAATCGAAAAG Chr16:17153824..17153843 60.04 45
downstream ENSMUSE00000703897 Chr16:17153403..17153607 AAGGTCACCACAAACCTGCT Chr16:17153499..17153518 59.62 50
downstream ENSMUSE00000517946 Chr16:17152106..17154375 GACGGCTTCTCTTTGTTTGC Chr16:17153637..17153656 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCTCTTCTGTAATCGCCTTGC Chr16:17167441..17167462 59.61 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCAGTAAGGCTAACCCGTGA Chr16:17167448..17167468 58.38 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CGCAAATGTGGAATGAAAAA Chr16:17167564..17167584 59.54 35 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CGCAAATGTGGAATGAAAAA Chr16:17167564..17167584 59.54 35 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000038965