Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7671
Trapped Gene
Csde1 (ENSMUSG00000068823)
Vector Insertion
Chr 3: 102824593 - 102832711
Public Clones (sanger) RRS061 (baygenomics) D001B07 (ggtc) H008A12 (ggtc) D043B12 (ggtc)
P111D01 (ggtc) P141H11 (ggtc) E060E02 (ggtc) D001B07 (ggtc) H008A12 (ggtc)
P009H12 (ggtc) P132D03 (ggtc) D145E02 (ggtc) D006E09 (ggtc) P145C07 (ggtc)
H002D05 (ggtc) D038H04 (ggtc) P082F07 (ggtc) P141H11 (ggtc) E056B05 (ggtc)
D001B07 (ggtc) (ggtc) P132D03 (ggtc) W058F05 (ggtc) H009G02 (ggtc)
D043B12 (ggtc) P111G04 (ggtc) P145C07 (ggtc) E060E02 (ggtc) D009C09 (ggtc)
3SE314A06 (ggtc) P065C06 (ggtc) P132D03 (ggtc) D145E02 (ggtc) (ggtc)
PST5212-NR (escells) PST21090-NL (escells) IST12580C11 (tigm) IST14616A5 (tigm)
IST14665G10 (tigm) IST14153F3 (tigm) IST14385F11 (tigm)
Private Clones OST452306 (lexicon) OST314762 (lexicon) OST314075 (lexicon) OST274956 (lexicon)
OST239461 (lexicon) OST215720 (lexicon) OST205750 (lexicon) OST204753 (lexicon)
OST148854 (lexicon) OST80929 (lexicon) OST37052 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000359109 (Chr3:102824530..102824592 +)
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
ENSMUSE00000359109 (Chr3:102824530..102824592 +)
Downstram Exon
ENSMUSE00000715379 (Chr3:102832712..102833135 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon ACTAGCAGCGTTGGGAAGTG Chr3:102832905..102832924 60.45 55

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

*** Putative Vector Insertion (Chr 3: 102824593 - 102832711) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000715379 Chr3:102832712..102833135 ACTAGCAGCGTTGGGAAGTG Chr3:102832905..102832924 60.45 55
downstream ENSMUSE00000716412 Chr3:102832712..102833135 ACTAGCAGCGTTGGGAAGTG Chr3:102832905..102832924 60.45 55
downstream ENSMUSE00000637043 Chr3:102842615..102842813 AACCCCAGTTTCACGAAGTG Chr3:102842704..102842723 60.01 50
downstream ENSMUSE00000671436 Chr3:102842615..102842813 AACCCCAGTTTCACGAAGTG Chr3:102842704..102842723 60.01 50
downstream ENSMUSE00000318141 Chr3:102843856..102843965 CAGTCCTCCGGTCAGATGAT Chr3:102843897..102843916 60.07 55
downstream ENSMUSE00000318135 Chr3:102844364..102844456 CTCCCTGTTGGACTCTGACC Chr3:102844437..102844456 59.68 60
downstream ENSMUSE00000318132 Chr3:102845068..102845165 TCCAGCTGAACATTCCCTTC Chr3:102845126..102845145 60.19 50
downstream ENSMUSE00000318128 Chr3:102847080..102847161 CGAGCCTGCTTCTTTTTCAA Chr3:102847136..102847155 60.63 45
downstream ENSMUSE00000318123 Chr3:102847480..102847608 TGAATTCCACGTCATCTCCA Chr3:102847594..102847613 60.05 45
downstream ENSMUSE00000318118 Chr3:102847729..102847854 TGACTGTTCCTTGAGGCAAT Chr3:102847780..102847799 58.29 45
downstream ENSMUSE00000318109 Chr3:102848552..102848764 GGTTGCTCGTTCCAATTTGT Chr3:102848713..102848732 59.98 45
downstream ENSMUSE00000318103 Chr3:102850708..102850848 GTGGAGCTGGTTCCCATCTA Chr3:102850818..102850837 60.07 55
downstream ENSMUSE00000318099 Chr3:102850937..102851101 TTTGCCTTTATTTGGGCTTG Chr3:102851098..102851117 60.07 40
downstream ENSMUSE00000318092 Chr3:102853544..102853651 TTCACCCCACAGTCGTCATA Chr3:102853590..102853609 59.96 50
downstream ENSMUSE00000372125 Chr3:102854221..102854396 GCCACATAACCCAAGAGACG Chr3:102854330..102854349 60.52 55
downstream ENSMUSE00000318079 Chr3:102854963..102855075 ACCATGTCTCCCAGTTCCAG Chr3:102855010..102855029 59.96 55
downstream ENSMUSE00000318072 Chr3:102856735..102856854 GAGGGCGAATGACTTTACCA Chr3:102856797..102856816 60.07 50
downstream ENSMUSE00000318065 Chr3:102858578..102858756 CCTACGAAGGGGTGTGATGT Chr3:102858732..102858751 59.84 55
downstream ENSMUSE00000173638 Chr3:102859272..102859435 CCAGTGCGCTGATTAAGGAT Chr3:102859405..102859424 60.24 50
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 AAATAATCGCCTTGCAGCAC Chr3:102827641..102827661 60.24 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGCTTACGTGACTGGGAAAA Chr3:102827638..102827658 59.32 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000068823