Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI21706
Trapped Gene
Hnrnpd (ENSMUSG00000000568)
Vector Insertion
Chr 5: 100396407 - 100405552
Public Clones D042H04 (ggtc) D051F02 (ggtc) D042H04 (ggtc) D156B03 (ggtc) CMHD-GT_505F4-3 (cmhd)
CMHD-GT_477B8-3 (cmhd)
Private Clones OST320485 (lexicon) OST313393 (lexicon) OST262178 (lexicon) OST147706 (lexicon)
OST67798 (lexicon) OST60489 (lexicon) OST57564 (lexicon) OST43218 (lexicon)
OST41439 (lexicon) OST39929 (lexicon) OST32413 (lexicon)
Severity of mutation (?) Insertion after 32% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000455342 (Chr5:100405553..100405609 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000455342 (Chr5:100405553..100405609 -)
Downstram Exon
ENSMUSE00000455322 (Chr5:100396238..100396406 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000484747 Chr5:100407411..100407957 No primer for this exon
upstream ENSMUSE00000455342 Chr5:100405553..100405609 No primer for this exon

*** Putative Vector Insertion (Chr 5: 100396407 - 100405552) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000455322 Chr5:100396238..100396406 No primer for this exon
downstream ENSMUSE00000188023 Chr5:100395041..100395202 No primer for this exon
downstream ENSMUSE00000188026 Chr5:100393689..100393820 No primer for this exon
downstream ENSMUSE00000188019 Chr5:100393003..100393102 No primer for this exon
downstream ENSMUSE00000188013 Chr5:100392750..100392896 No primer for this exon
downstream ENSMUSE00000542064 Chr5:100391534..100391631 No primer for this exon
downstream ENSMUSE00000482498 Chr5:100390028..100390352 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCACTTCTTGGCAACTTCT Chr5:100396513..100396533 59.48 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCACTTCTTGGCAACTTCT Chr5:100396513..100396533 59.48 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TCCCGGGACTAGACTGGAAT Chr5:100396601..100396621 60.84 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 ACAGAAGCGTGACTGGGAAA Chr5:100396546..100396566 60.83 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000000568