Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13759
Trapped Gene
Zc3h6 (ENSMUSG00000042851)
Vector Insertion
Chr 2: 128793573 - 128816826
Public Clones (ggtc) CMHD-GT_270F8-3 (cmhd) IST10045A7 (tigm)
Private Clones OST341322 (lexicon) OST318781 (lexicon) OST318769 (lexicon) OST288198 (lexicon)
OST258058 (lexicon) OST250352 (lexicon) OST138651 (lexicon) OST129967 (lexicon)
OST84489 (lexicon) OST44723 (lexicon) OST44698 (lexicon) OST38316 (lexicon)
OST34520 (lexicon)
Severity of mutation (?) Insertion after 1% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000683516 (Chr2:128793143..128793572 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATCTCTCTGGCGTTGGTTGT Chr2:128793324..128793343 59.73 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000683516 (Chr2:128793143..128793572 +)
Downstram Exon
ENSMUSE00000314964 (Chr2:128816827..128817007 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATCTCTCTGGCGTTGGTTGT Chr2:128793324..128793343 59.73 50 CTCGTGTTTCCTCCTTTTGG Chr2:128817001..128817020 59.71 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000683516 Chr2:128793143..128793572 ATCTCTCTGGCGTTGGTTGT Chr2:128793324..128793343 59.73 50

*** Putative Vector Insertion (Chr 2: 128793573 - 128816826) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000314964 Chr2:128816827..128817007 CTCGTGTTTCCTCCTTTTGG Chr2:128817001..128817020 59.71 50
downstream ENSMUSE00000169100 Chr2:128818895..128819017 TTACGGGAACTTTGCATACG Chr2:128818974..128818993 58.7 45
downstream ENSMUSE00000683513 Chr2:128819115..128819234 GAACCACAGTGATGGCTGAA Chr2:128819139..128819158 59.68 50
downstream ENSMUSE00000415838 Chr2:128823341..128823608 GAGAACGATGACCCTGAGGA Chr2:128823567..128823586 60.2 55
downstream ENSMUSE00000415835 Chr2:128827878..128828014 TTCTTCGGCAAAAGATGTCC Chr2:128827938..128827957 60.19 45
downstream ENSMUSE00000411756 Chr2:128831732..128831848 TCCACTTTTTCCCTGGTTTG Chr2:128831759..128831778 59.94 45
downstream ENSMUSE00000169083 Chr2:128832449..128832560 No primer for this exon
downstream ENSMUSE00000363510 Chr2:128836152..128836261 TTGGTAGCACTTTGCTCCACT Chr2:128836200..128836220 59.93 47.62
downstream ENSMUSE00000404496 Chr2:128837403..128837656 GAGTTATGCCGCGTTTCCTA Chr2:128837481..128837500 60.23 50
downstream ENSMUSE00000355717 Chr2:128840072..128840574 CCTCAAACTGTGGTCCTGGT Chr2:128840124..128840143 60 55
downstream ENSMUSE00000334899 Chr2:128841136..128841369 GTCAACGGGATGAAAAGAGC Chr2:128841304..128841323 59.68 50
downstream ENSMUSE00000683515 Chr2:128841858..128843320 AGTGGGGGCAGAGGTAAGTT Chr2:128842488..128842507 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGTTTAGATTCAGAAATGCCAAC Chr2:128793530..128793553 58.31 34.78 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTTTAGATTCAGAAATGCCAAC Chr2:128793530..128793553 58.31 34.78 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042851