Tools for the biologist enabling optimized use of gene trap clones

  Homepage | Blast Search | GO Search | Advanced Search | About

UniTrap UNI5103
Trapped Gene
Ncaph (ENSMUSG00000034906)
Vector Insertion
Chr 2: 126959584 - 126959653
Public Clones YTC737 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000719334 (Chr2:126959585..126959652 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTTACTCCGGAGACGTGGAG Chr2:126959610..126959629 59.86 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000719334 (Chr2:126959585..126959652 -)
Downstram Exon
ENSMUSE00000708433 (Chr2:126959585..126959652 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTTACTCCGGAGACGTGGAG Chr2:126959610..126959629 59.86 60 ATCTTGCTCTCCACGTCTCC Chr2:126959580..126959599 59.41 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000708433 Chr2:126959585..126959652 CTTACTCCGGAGACGTGGAG Chr2:126959610..126959629 59.86 60
upstream ENSMUSE00000719334 Chr2:126959585..126959652 CTTACTCCGGAGACGTGGAG Chr2:126959610..126959629 59.86 60

*** Putative Vector Insertion (Chr 2: 126959584 - 126959653) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000320738 Chr2:126953221..126953458 CTTCGAGGACTGGGGTTTTA Chr2:126953305..126953324 59.17 50
downstream ENSMUSE00000683747 Chr2:126953221..126953458 CTTCGAGGACTGGGGTTTTA Chr2:126953305..126953324 59.17 50
downstream ENSMUSE00000320729 Chr2:126952840..126952930 No primer for this exon
downstream ENSMUSE00000320721 Chr2:126951851..126951943 AATCAAATGCAAGCCGAAAG Chr2:126951883..126951902 60.21 40
downstream ENSMUSE00000320713 Chr2:126951287..126951422 CATCCACACGGACAGCATAG Chr2:126951346..126951365 60.14 55
downstream ENSMUSE00000320704 Chr2:126950567..126950691 TGTTCAATGGTTTTGCAGGA Chr2:126950591..126950610 60.09 40
downstream ENSMUSE00000320698 Chr2:126949273..126949462 GCAGCGTGGAGAGAAATACC Chr2:126949365..126949384 59.84 55
downstream ENSMUSE00000320691 Chr2:126947776..126947867 ATGTGTTTCGCTGTCCCATT Chr2:126947760..126947779 60.38 45
downstream ENSMUSE00000320681 Chr2:126946861..126947063 CTCCGGAACTCTTCATGGTC Chr2:126946872..126946891 59.65 55
downstream ENSMUSE00000320672 Chr2:126943813..126943961 TCCCCAGGTTTCATGGATAA Chr2:126943868..126943887 60.13 45
downstream ENSMUSE00000320665 Chr2:126943242..126943348 TGTGCTCTGTGCAGGAGGTA Chr2:126943300..126943319 60.62 55
downstream ENSMUSE00000320657 Chr2:126942268..126942390 TGGCTTTCCAATTCTGGTTC Chr2:126942317..126942336 60.05 45
downstream ENSMUSE00000320650 Chr2:126939296..126939406 AGTTGGAGGTGTCGTTAGGG Chr2:126939291..126939310 59.06 55
downstream ENSMUSE00000320646 Chr2:126934221..126934394 TGGATCCGCAAATAAATCGT Chr2:126934325..126934344 60.29 40
downstream ENSMUSE00000320639 Chr2:126933090..126933206 TTTGGCAGTCTTGGCGTAAT Chr2:126933146..126933165 60.64 45
downstream ENSMUSE00000320635 Chr2:126931840..126931931 TTGTCTGCAGGTCCTTTGTG Chr2:126931819..126931838 59.87 50
downstream ENSMUSE00000320629 Chr2:126931582..126931657 AAAGCCAGGGGTATGGAGAG Chr2:126931591..126931610 60.46 55
downstream ENSMUSE00000346917 Chr2:126929567..126930016 GTGGGACGGTCACAGAAAGT Chr2:126929683..126929702 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAGTAATCGCCTTGCAGCAC Chr2:126959585..126959605 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACTTACTCCGGAGACGTGGA Chr2:126959609..126959629 59.72 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034906