Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14634
Trapped Gene
Spats1 (ENSMUSG00000023935)
Vector Insertion
Chr 17: 45586383 - 45589690
Public Clones (sanger) (sanger) FHCRC-GT-S4-2C1 (fhcrc) PST1696 (escells) PST18961-NR (escells)
IST10525E9 (tigm) IST13749A7 (tigm) IST12598F7 (tigm) IST14710H8 (tigm)
IST14094D11 (tigm) IST13206H3 (tigm) IST12767D1 (tigm) IST12943H4 (tigm)
IST14094D11 (tigm) IST13891G9 (tigm) IST15109B7 (tigm) IST10556C4 (tigm)
IST12147H10 (tigm) IST11858A3 (tigm) IST12388G10 (tigm) IST12943H4 (tigm)
IST12486A10 (tigm) IST15109B7 (tigm) IST14733E5 (tigm)
Private Clones OST449063 (lexicon) OST411133 (lexicon) OST320826 (lexicon) OST200443 (lexicon)
OST182881 (lexicon) OST139721 (lexicon) OST127203 (lexicon) OST68998 (lexicon)
OST63095 (lexicon) OST61995 (lexicon) OST60805 (lexicon) OST37715 (lexicon)
OST32797 (lexicon)
Severity of mutation (?) Insertion after 85% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000657300 (Chr17:45589627..45589689 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACTTGAGCCACTTCCAAAA Chr17:45589635..45589654 58.9 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000657300 (Chr17:45589627..45589689 -)
Downstram Exon
ENSMUSE00000657299 (Chr17:45586384..45586499 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACTTGAGCCACTTCCAAAA Chr17:45589635..45589654 58.9 45 CTGCCAGTTGTCAAGCTCCT Chr17:45586399..45586418 60.59 55

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
upstream ENSMUSE00000657301 Chr17:45591040..45591160 ATGGAATCCCCAAATTGACA Chr17:45591126..45591145 59.99 40
upstream ENSMUSE00000657300 Chr17:45589627..45589689 CACTTGAGCCACTTCCAAAA Chr17:45589635..45589654 58.9 45
upstream ENSMUSE00000657299 Chr17:45586384..45586499 TGCCCTTCCTACATGGTTTC Chr17:45586394..45586413 59.93 50

*** Putative Vector Insertion (Chr 17: 45586383 - 45589690) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 GAGCCACTTTAATCGCCTTG Chr17:45586628..45586648 59.85 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTTGAGCCACTTCGTGACTG Chr17:45586631..45586651 59.62 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TTAATGTGGAGGCCTCGTTC Chr17:45589600..45589620 60.07 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TTAATGTGGAGGCCTCGTTC Chr17:45589600..45589620 60.07 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000023935