Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3596
Trapped Gene
Mrps27 (ENSMUSG00000041632)
Vector Insertion
Chr 13: 100118365 - 100132919
Public Clones (sanger) (sanger) BB0744 (sanger) YTC271 (baygenomics) HMA485 (baygenomics)
(ggtc) (ggtc) (ggtc)
Private Clones OST435461 (lexicon) OST262830 (lexicon) OST262208 (lexicon) OST82131 (lexicon)
OST31073 (lexicon)
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000294492 (Chr13:100118287..100118364 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAAAGATGCCTGCTTTCTGC Chr13:100118289..100118308 59.6 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000294492 (Chr13:100118287..100118364 +)
Downstram Exon
ENSMUSE00000294486 (Chr13:100132920..100132990 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAAAGATGCCTGCTTTCTGC Chr13:100118289..100118308 59.6 45 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000294499 Chr13:100114745..100114830 No primer for this exon
upstream ENSMUSE00000294492 Chr13:100118287..100118364 AAAAGATGCCTGCTTTCTGC Chr13:100118289..100118308 59.6 45

*** Putative Vector Insertion (Chr 13: 100118365 - 100132919) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000294486 Chr13:100132920..100132990 No primer for this exon
downstream ENSMUSE00000294479 Chr13:100135180..100135238 ATCTTCTCGGGATGCAATGT Chr13:100135212..100135231 59.51 45
downstream ENSMUSE00000294474 Chr13:100170217..100170331 CAGTTGGGACTGTGTCGAAAT Chr13:100170239..100170259 60.02 47.62
downstream ENSMUSE00000294469 Chr13:100173459..100173537 No primer for this exon
downstream ENSMUSE00000294465 Chr13:100174943..100175058 GTGAGCTCCGTCTTCTCTGC Chr13:100175060..100175079 60.29 60
downstream ENSMUSE00000407388 Chr13:100179764..100179866 AACTCAGGCCCACTGTGTTC Chr13:100179842..100179861 60.16 55
downstream ENSMUSE00000433773 Chr13:100181233..100181375 CATCACTTGGAGGGCTCTGT Chr13:100181330..100181349 60.26 55
downstream ENSMUSE00000294446 Chr13:100182150..100182320 CACCACCTTCAGGACTCCAT Chr13:100182185..100182204 59.96 55
downstream ENSMUSE00000374496 Chr13:100184694..100185517 CTGTCCTGGCTGAACACTGA Chr13:100184972..100184991 60.02 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGTTTTTAATCGCCTTGCAG Chr13:100118410..100118430 58.96 40 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTTTTCGTGACTGGGAAAACC Chr13:100127411..100127432 60.75 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000041632