Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI24470
Trapped Gene
Mrps27 (ENSMUSG00000041632)
Vector Insertion
Chr 13: 100132991 - 100135179
Public Clones IST10979D1 (tigm)
Private Clones OST218740 (lexicon)
Severity of mutation (?) Insertion after 18% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000294486 (Chr13:100132920..100132990 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCATCCTTAATGGACAAAGC Chr13:100132927..100132947 60.09 42.86 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000294486 (Chr13:100132920..100132990 +)
Downstram Exon
ENSMUSE00000294479 (Chr13:100135180..100135238 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCATCCTTAATGGACAAAGC Chr13:100132927..100132947 60.09 42.86 ATCTTCTCGGGATGCAATGT Chr13:100135212..100135231 59.51 45

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
upstream ENSMUSE00000294486 Chr13:100132920..100132990 TGCATCCTTAATGGACAAAGC Chr13:100132927..100132947 60.09 42.86

*** Putative Vector Insertion (Chr 13: 100132991 - 100135179) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TATAATCGCCTTGCAGCACA Chr13:100133040..100133060 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTACGTGACTGGGAAAACC Chr13:100133038..100133058 58.47 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000041632