Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13979
Trapped Gene
Sdsl (ENSMUSG00000029596)
Vector Insertion
Chr 5: 120908561 - 120909453
Public Clones CMHD-GT_181H9-3 (cmhd) CMHD-GT_181E11-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 81% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000190538 (Chr5:120909454..120909578 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTAGAAGACCGGGAGGCTGT Chr5:120909477..120909496 60.65 60 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000190538 (Chr5:120909454..120909578 -)
Downstram Exon
ENSMUSE00000413622 (Chr5:120908212..120908560 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTAGAAGACCGGGAGGCTGT Chr5:120909477..120909496 60.65 60 CACAGGATGCCCGAGTAGAT Chr5:120908469..120908488 60.1 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000288583 Chr5:120922735..120922819 GTCTCACGTGGCTTCGTTCT Chr5:120922738..120922757 60.45 55
upstream ENSMUSE00000343830 Chr5:120922730..120922772 GTCTCACGTGGCTTCGTTCT Chr5:120922738..120922757 60.45 55
upstream ENSMUSE00000288577 Chr5:120917283..120917507 TGAGCTGCGTAAGGAAGACA Chr5:120917463..120917482 59.74 50
upstream ENSMUSE00000288568 Chr5:120913041..120913234 CCTTTAAGATTCGGGGCATC Chr5:120913059..120913078 60.76 50
upstream ENSMUSE00000708223 Chr5:120913041..120913234 CCTTTAAGATTCGGGGCATC Chr5:120913059..120913078 60.76 50
upstream ENSMUSE00000190550 Chr5:120912855..120912894 GACATCTGGTGTGCTCCTCA Chr5:120912856..120912875 59.83 55
upstream ENSMUSE00000288552 Chr5:120911986..120912125 No primer for this exon
upstream ENSMUSE00000288542 Chr5:120910616..120910704 CCGTTTGACCATCCCCTTAT Chr5:120910619..120910638 60.93 50
upstream ENSMUSE00000190544 Chr5:120909765..120909992 ACAGTTTCAATTCGGCCTTG Chr5:120909803..120909822 60.11 45
upstream ENSMUSE00000190538 Chr5:120909454..120909578 GTAGAAGACCGGGAGGCTGT Chr5:120909477..120909496 60.65 60

*** Putative Vector Insertion (Chr 5: 120908561 - 120909453) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000413622 Chr5:120908212..120908560 CACAGGATGCCCGAGTAGAT Chr5:120908469..120908488 60.1 55
downstream ENSMUSE00000538844 Chr5:120908211..120908560 CACAGGATGCCCGAGTAGAT Chr5:120908469..120908488 60.1 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGGCCTGGCACTCTATTCAC Chr5:120909425..120909445 59.31 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGGCCTGGCACTCTATTCAC Chr5:120909425..120909445 59.31 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029596