Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14557
Trapped Gene
4933406E20Rik (ENSMUSG00000006675)
Vector Insertion
Chr 9: 108485972 - 108499312
Public Clones FHCRC-GT-S6-2E1 (fhcrc) IST12739C12 (tigm) IST12743B2 (tigm) IST15051G10 (tigm)
IST13244H7 (tigm) IST10453E1 (tigm) IST13004E6 (tigm) IST10314A3 (tigm)
IST11380F12 (tigm) IST12447D7 (tigm) IST10174E4 (tigm) IST12354D11 (tigm)
IST10807B10 (tigm) IST10649D8 (tigm) IST12865D1 (tigm) IST12447D7 (tigm)
IST12354D11 (tigm) IST10649D8 (tigm) IST11522A8 (tigm) IST11931F7 (tigm)
IST10407H1 (tigm)
Private Clones OST442489 (lexicon) OST440578 (lexicon) OST429869 (lexicon) OST425260 (lexicon)
OST402305 (lexicon) OST390795 (lexicon) OST379611 (lexicon) OST367836 (lexicon)
OST360970 (lexicon) OST354834 (lexicon) OST308276 (lexicon) OST300962 (lexicon)
OST279817 (lexicon) OST220766 (lexicon) OST176552 (lexicon) OST176516 (lexicon)
OST162497 (lexicon) OST149468 (lexicon) OST134794 (lexicon)
Severity of mutation (?) Insertion after 29% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000240493 (Chr9:108499230..108499311 -)
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
ENSMUSE00000240493 (Chr9:108499230..108499311 -)
Downstram Exon
ENSMUSE00000583242 (Chr9:108485973..108486163 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000221368 Chr9:108499539..108499931 No primer for this exon
upstream ENSMUSE00000240493 Chr9:108499230..108499311 No primer for this exon
upstream ENSMUSE00000583242 Chr9:108485973..108486163 No primer for this exon

*** Putative Vector Insertion (Chr 9: 108485972 - 108499312) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000583241 Chr9:108485178..108485274 No primer for this exon
downstream ENSMUSE00000583240 Chr9:108484173..108484335 No primer for this exon
downstream ENSMUSE00000583239 Chr9:108483050..108483235 No primer for this exon
downstream ENSMUSE00000583238 Chr9:108482347..108482437 No primer for this exon
downstream ENSMUSE00000583237 Chr9:108482047..108482170 No primer for this exon
downstream ENSMUSE00000583236 Chr9:108481157..108481639 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATAATCGCCTTGCAGCAC Chr9:108496244..108496264 58.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACCACACCATGCTGAGAACA Chr9:108496295..108496315 60.16 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCGCTGCTTTTTGGTAAGTC Chr9:108496221..108496241 59.88 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GTCCACGTGACTGGGAAAAC Chr9:108499163..108499183 60.41 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000006675