Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20370
Trapped Gene
Nde1 (ENSMUSG00000022678)
Vector Insertion
Chr 16: 14192434 - 14192922
Public Clones not available
Private Clones OST365387 (lexicon)
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000388059 (Chr16:14191811..14192921 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AATGCCAGCTCGTCTCTCAT Chr16:14192648..14192667 59.98 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000388059 (Chr16:14191811..14192921 +)
Downstram Exon
ENSMUSE00000717321 (Chr16:14192435..14192921 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AATGCCAGCTCGTCTCTCAT Chr16:14192648..14192667 59.98 50 CCCTGGTTGCTCTATGGTGT Chr16:14192578..14192597 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000710851 Chr16:14163380..14163461 No primer for this exon
upstream ENSMUSE00000396125 Chr16:14163399..14163461 No primer for this exon
upstream ENSMUSE00000360932 Chr16:14169545..14169668 CCTGGCCATGACCTACAAAC Chr16:14169645..14169664 60.38 55
upstream ENSMUSE00000710553 Chr16:14169545..14169668 CCTGGCCATGACCTACAAAC Chr16:14169645..14169664 60.38 55
upstream ENSMUSE00000704198 Chr16:14169568..14169668 TGGCCATGACCTACAAACAG Chr16:14169647..14169666 59.57 50
upstream ENSMUSE00000563156 Chr16:14170431..14170584 AGCCGAGAATACGAAGCTGA Chr16:14170474..14170493 60.12 50
upstream ENSMUSE00000704197 Chr16:14170431..14170584 AGCCGAGAATACGAAGCTGA Chr16:14170474..14170493 60.12 50
upstream ENSMUSE00000129431 Chr16:14175384..14175532 TGACCTGGAAAGAGCCAAAC Chr16:14175512..14175531 60.23 50
upstream ENSMUSE00000563152 Chr16:14183569..14183705 AGCGTTTGAATCAAGCCATT Chr16:14183601..14183620 59.71 40
upstream ENSMUSE00000704196 Chr16:14183569..14183705 AGCGTTTGAATCAAGCCATT Chr16:14183601..14183620 59.71 40
upstream ENSMUSE00000129434 Chr16:14185787..14185966 CCACAGGCTCTGTACCGTCT Chr16:14185886..14185905 60.32 60
upstream ENSMUSE00000129433 Chr16:14188406..14188497 CCGGATATCAGCCCTAAACA Chr16:14188449..14188468 59.92 50
upstream ENSMUSE00000129429 Chr16:14190180..14190325 CTCAGGACGAGGAACCAAAA Chr16:14190254..14190273 60.22 50
upstream ENSMUSE00000704199 Chr16:14191683..14191695 No primer for this exon
upstream ENSMUSE00000388059 Chr16:14191811..14192921 AATGCCAGCTCGTCTCTCAT Chr16:14192648..14192667 59.98 50
upstream ENSMUSE00000704195 Chr16:14191811..14192659 TTGAGATCCCTTCCCTGATG Chr16:14192430..14192449 60 50

*** Putative Vector Insertion (Chr 16: 14192434 - 14192922) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000717321 Chr16:14192435..14192921 CCCTGGTTGCTCTATGGTGT Chr16:14192578..14192597 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGAGATCCCTTCCCTGATG Chr16:14192431..14192451 60 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGAGATCCCTTCCCTGATG Chr16:14192431..14192451 60 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000022678