Tools for the biologist enabling optimized use of gene trap clones

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

UniTrap UNI4799
Trapped Gene
Csde1 (ENSMUSG00000068823)
Vector Insertion
Chr 3: 102859436 - 102860267
Public Clones AS0325 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 93% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000173638 (Chr3:102859272..102859435 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAGTTCAGGATGGCGTTGAG Chr3:102859330..102859349 60.26 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000173638 (Chr3:102859272..102859435 +)
Downstram Exon
ENSMUSE00000173639 (Chr3:102860268..102860400 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAGTTCAGGATGGCGTTGAG Chr3:102859330..102859349 60.26 50 CTTGGCTGACGAAGAACCAT Chr3:102860384..102860403 60.26 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000359109 Chr3:102824530..102824592 No primer for this exon
upstream ENSMUSE00000715379 Chr3:102832712..102833135 CACTTCCCAACGCTGCTAGT Chr3:102832883..102832902 60.45 55
upstream ENSMUSE00000716412 Chr3:102832712..102833135 CACTTCCCAACGCTGCTAGT Chr3:102832883..102832902 60.45 55
upstream ENSMUSE00000637043 Chr3:102842615..102842813 TCAGTGTTCAGAACGGCAAG Chr3:102842734..102842753 60.03 50
upstream ENSMUSE00000671436 Chr3:102842615..102842813 TCAGTGTTCAGAACGGCAAG Chr3:102842734..102842753 60.03 50
upstream ENSMUSE00000318141 Chr3:102843856..102843965 ATCATCTGACCGGAGGACTG Chr3:102843875..102843894 60.07 55
upstream ENSMUSE00000318135 Chr3:102844364..102844456 GCGCTGTTCCTCACAACTTA Chr3:102844371..102844390 59.08 50
upstream ENSMUSE00000318132 Chr3:102845068..102845165 GAATGTTCAGCTGGAAACTGG Chr3:102845109..102845129 59.73 47.62
upstream ENSMUSE00000318128 Chr3:102847080..102847161 GGCTCGCTGTCAAGGAGTAG Chr3:102847128..102847147 60.16 60
upstream ENSMUSE00000318123 Chr3:102847480..102847608 TACAGCCTGGAGATGACGTG Chr3:102847565..102847584 59.85 55
upstream ENSMUSE00000318118 Chr3:102847729..102847854 TGCCTCAAGGAACAGTCATTT Chr3:102847760..102847780 59.73 42.86
upstream ENSMUSE00000318109 Chr3:102848552..102848764 AATTGGAACGAGCAACCAAC Chr3:102848694..102848713 59.98 45
upstream ENSMUSE00000318103 Chr3:102850708..102850848 CTAGATGGGAACCAGCTCCA Chr3:102850795..102850814 60.21 55
upstream ENSMUSE00000318099 Chr3:102850937..102851101 CTGGGCACCGTAGAAAAAGA Chr3:102851030..102851049 60.24 50
upstream ENSMUSE00000318092 Chr3:102853544..102853651 TATGACGACTGTGGGGTGAA Chr3:102853568..102853587 59.96 50
upstream ENSMUSE00000372125 Chr3:102854221..102854396 TGCAACTTGCGTGAGACTTT Chr3:102854265..102854284 59.64 45
upstream ENSMUSE00000318079 Chr3:102854963..102855075 CTGGAACTGGGAGACATGGT Chr3:102854988..102855007 59.96 55
upstream ENSMUSE00000318072 Chr3:102856735..102856854 TGAGGAAGCTAATCCCACCA Chr3:102856748..102856767 60.59 50
upstream ENSMUSE00000318065 Chr3:102858578..102858756 CAAAGGGGATTGCCTACAGA Chr3:102858627..102858646 60.07 50
upstream ENSMUSE00000173638 Chr3:102859272..102859435 AAGTTCAGGATGGCGTTGAG Chr3:102859330..102859349 60.26 50

*** Putative Vector Insertion (Chr 3: 102859436 - 102860267) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000173639 Chr3:102860268..102860400 CTTGGCTGACGAAGAACCAT Chr3:102860384..102860403 60.26 50
downstream ENSMUSE00000507197 Chr3:102860809..102862108 GGAACCACGGGGCTATTTAT Chr3:102861771..102861790 60.04 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATCTAATCGCCTTGCAGCAC Chr3:102859484..102859504 60.38 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCTGTAATGTCTGGCGAGT Chr3:102859414..102859434 60.28 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000068823