Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14987
Trapped Gene
Spats1 (ENSMUSG00000023935)
Vector Insertion
Chr 17: 45594106 - 45598260
Public Clones (sanger) (sanger) (sanger) (sanger) (sanger) (sanger)
(sanger) (sanger) (sanger) (sanger) (sanger) (sanger)
(sanger) CMHD-GT_518A1-5S (cmhd) PST8934-NR (escells) IST13352D5 (tigm)
IST15106H11 (tigm) IST14517G12 (tigm) IST11669C12 (tigm) IST14861F9 (tigm)
IST14928G6 (tigm) IST10912H11HMF1 (tigm) IST14982F2 (tigm) IST14861F9 (tigm)
IST14335C8 (tigm) IST13874C6 (tigm) IST14931A9 (tigm) IST11098B11 (tigm)
IST11863C8 (tigm) IST13740B2 (tigm) IST12666G12 (tigm) IST10978A8 (tigm)
IST10954H7 (tigm) IST14079C1 (tigm) IST14663B6 (tigm) IST12024G12 (tigm)
IST11045G5 (tigm) IST12815A7 (tigm) IST12086H8 (tigm) IST13363G11 (tigm)
IST12024G12 (tigm)
Private Clones OST471450 (lexicon) OST446109 (lexicon) OST379215 (lexicon) OST173494 (lexicon)
OST168219 (lexicon) OST103447 (lexicon) OST50534 (lexicon) OST47089 (lexicon)
OST35418 (lexicon) OST32327 (lexicon)
Severity of mutation (?) Insertion after 48% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000657303 (Chr17:45598111..45598259 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAAAGTTTCGCTGCCTGAAA Chr17:45598162..45598181 60 40 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000657303 (Chr17:45598111..45598259 -)
Downstram Exon
ENSMUSE00000657302 (Chr17:45594107..45594268 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAAAGTTTCGCTGCCTGAAA Chr17:45598162..45598181 60 40 GGATGTTGCTGCTGAACCTT Chr17:45594193..45594212 60.26 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000696133 Chr17:45611748..45611893 GCATCCTGGTATTTGGCAGT Chr17:45611804..45611823 59.96 50
upstream ENSMUSE00000696141 Chr17:45603643..45603655 No primer for this exon
upstream ENSMUSE00000696132 Chr17:45601376..45601529 GACCAGCCTCTCGTCTTCTG Chr17:45601437..45601456 60.13 60
upstream ENSMUSE00000696140 Chr17:45601376..45601532 GACCAGCCTCTCGTCTTCTG Chr17:45601437..45601456 60.13 60
upstream ENSMUSE00000657303 Chr17:45598111..45598259 AAAAGTTTCGCTGCCTGAAA Chr17:45598162..45598181 60 40
upstream ENSMUSE00000657302 Chr17:45594107..45594268 GCGTCCTGAGTGGACATTTT Chr17:45594239..45594258 60.12 50

*** Putative Vector Insertion (Chr 17: 45594106 - 45598260) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000657301 Chr17:45591040..45591160 GGATTATCCCCTGGTGTCAA Chr17:45591090..45591109 59.6 50
downstream ENSMUSE00000657300 Chr17:45589627..45589689 TTTTGGAAGTGGCTCAAGTG Chr17:45589613..45589632 58.9 45
downstream ENSMUSE00000657299 Chr17:45586384..45586499 CTGCCAGTTGTCAAGCTCCT Chr17:45586399..45586418 60.59 55
downstream ENSMUSE00000657297 Chr17:45585886..45586140 GTGTTCAACAAGGCCAAACA Chr17:45585934..45585953 59.59 45
downstream ENSMUSE00000657298 Chr17:45582830..45583032 ATGAGAGGATGTCCGGTGAG Chr17:45582856..45582875 60.07 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAACCCTTCCACTTGCCTTC Chr17:45598261..45598281 59.17 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAACCCTTCCACTTGCCTTC Chr17:45598261..45598281 59.17 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GACCTTTCTAATCGCCTTGC Chr17:45598047..45598067 58.93 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CTTTCCGTGACTGGGAAAAC Chr17:45598044..45598064 59.57 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000023935