Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13226
Trapped Gene
Hip2 (ENSMUSG00000029203)
Vector Insertion
Chr 5: 65928786 - 65957227
Public Clones (sanger) (sanger) E086E06 (ggtc) E127E05 (ggtc) E127E05 (ggtc)
CMHD-GT_346H11-3 (cmhd) IST14923F1 (tigm) IST14583D3 (tigm) IST14377A8 (tigm)
IST15060C11 (tigm) IST14909B7 (tigm)
Private Clones OST473287 (lexicon) OST468101 (lexicon) OST458086 (lexicon) OST443364 (lexicon)
OST435006 (lexicon) OST422636 (lexicon) OST416660 (lexicon) OST413535 (lexicon)
OST402504 (lexicon) OST355737 (lexicon) OST336626 (lexicon) OST319414 (lexicon)
OST307153 (lexicon) OST285744 (lexicon) OST283254 (lexicon) OST265990 (lexicon)
OST261668 (lexicon) OST234818 (lexicon) OST217343 (lexicon) OST189192 (lexicon)
OST187821 (lexicon) OST168225 (lexicon) OST165704 (lexicon) OST162815 (lexicon)
OST148516 (lexicon) OST145581 (lexicon) OST142088 (lexicon) OST124768 (lexicon)
OST100427 (lexicon) OST63539 (lexicon) OST31754 (lexicon) OST28718 (lexicon)
OST28446 (lexicon) OST27374 (lexicon) OST24782 (lexicon) OST23237 (lexicon)
OST23205 (lexicon) OST21858 (lexicon) OST17607 (lexicon) OST14200 (lexicon)
OST8431 (lexicon) OST5569 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000716543 (Chr5:65928539..65928785 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGCGGAGGTGATTCTACAGT Chr5:65928545..65928564 60.28 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000716543 (Chr5:65928539..65928785 +)
Downstram Exon
ENSMUSE00000254368 (Chr5:65957228..65957321 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGCGGAGGTGATTCTACAGT Chr5:65928545..65928564 60.28 55 GTGTGTCTGGAGGTCCTGCT Chr5:65957315..65957334 60.31 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000716543 Chr5:65928539..65928785 CGCGGAGGTGATTCTACAGT Chr5:65928545..65928564 60.28 55
upstream ENSMUSE00000254377 Chr5:65928570..65928785 GAATCAAGCGGGAGTTCAAG Chr5:65928745..65928764 59.81 50

*** Putative Vector Insertion (Chr 5: 65928786 - 65957227) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000254368 Chr5:65957228..65957321 GTGTGTCTGGAGGTCCTGCT Chr5:65957315..65957334 60.31 60
downstream ENSMUSE00000254358 Chr5:65962771..65962829 No primer for this exon
downstream ENSMUSE00000254349 Chr5:65972625..65972707 AACAAATAGCCCCTGTGACG Chr5:65972688..65972707 59.99 50
downstream ENSMUSE00000186857 Chr5:65983115..65983214 ACAATAATACCGTGCGCAGA Chr5:65983152..65983171 59.21 45
downstream ENSMUSE00000186858 Chr5:65985659..65985787 GTACACGTGTGCCCAAAGTC Chr5:65985718..65985737 59.06 55
downstream ENSMUSE00000254330 Chr5:65986114..65986379 CAGCTCCTGTGCCTCAGTTA Chr5:65986204..65986223 59.19 55
downstream ENSMUSE00000710549 Chr5:65986114..65987632 TGAGAATCTCCGCTCTGGAT Chr5:65986775..65986794 59.91 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AATATAATCGCCTTGCAGCAC Chr5:65955833..65955854 59.25 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAAATACGTGACTGGGAAAACC Chr5:65955831..65955853 59.29 40.91 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029203