Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8886
Trapped Gene
Rbm6 (ENSMUSG00000032582)
Vector Insertion
Chr 9: 107680359 - 107681904
Public Clones XL018 (baygenomics) XL002 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 88% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000250644 (Chr9:107681905..107681979 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCAAGAGCTCGCCTATCTG Chr9:107681923..107681942 59.88 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000250644 (Chr9:107681905..107681979 -)
Downstram Exon
ENSMUSE00000250611 (Chr9:107680261..107680358 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCAAGAGCTCGCCTATCTG Chr9:107681923..107681942 59.88 55 CCCTTCGGTCATTTCCTTTT Chr9:107680303..107680322 60.29 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000634400 Chr9:107774980..107775038 No primer for this exon
upstream ENSMUSE00000691183 Chr9:107774980..107775152 No primer for this exon
upstream ENSMUSE00000454980 Chr9:107762680..107762790 ACCACCGTGCTAGAGTTTGG Chr9:107762769..107762788 60.17 55
upstream ENSMUSE00000221165 Chr9:107754456..107756005 TTTCTCAGGGCAAAATGTCC Chr9:107754480..107754499 60.05 45
upstream ENSMUSE00000691182 Chr9:107754456..107755734 TTTCTCAGGGCAAAATGTCC Chr9:107754480..107754499 60.05 45
upstream ENSMUSE00000221168 Chr9:107753246..107753335 CCAAGCGAGGAGAAACCTAA Chr9:107753295..107753314 59.45 50
upstream ENSMUSE00000221163 Chr9:107749599..107749668 TGCCTTTCGAACTTCTGATG Chr9:107749641..107749660 59 45
upstream ENSMUSE00000454954 Chr9:107735765..107735838 TATGGCTATGTCTGCGTGGA Chr9:107735811..107735830 60.24 50
upstream ENSMUSE00000221167 Chr9:107703030..107703104 CCAAGCCCAGATTTTTGGTA Chr9:107703040..107703059 59.93 45
upstream ENSMUSE00000221166 Chr9:107698808..107698868 ACTGGTGGGCATCAGTCTTC Chr9:107698837..107698856 60.12 55
upstream ENSMUSE00000221161 Chr9:107694083..107694349 GAGCCATGGTCTGGAGATTC Chr9:107694106..107694125 59.62 55
upstream ENSMUSE00000250818 Chr9:107693336..107693496 AGCCCTACGTGCATCTCACT Chr9:107693417..107693436 59.9 55
upstream ENSMUSE00000250794 Chr9:107691939..107692036 GTAAACCTGGCCACTGGAAA Chr9:107691945..107691964 59.97 50
upstream ENSMUSE00000454923 Chr9:107690661..107690703 AAATGATTCTGGGGACCATTC Chr9:107690683..107690703 60.01 42.86
upstream ENSMUSE00000250753 Chr9:107690439..107690520 AAATCGACAAGGGCAACAGT Chr9:107690439..107690458 59.6 45
upstream ENSMUSE00000334993 Chr9:107690110..107690195 ACCCCTTGGCAGGAACTTAC Chr9:107690128..107690147 60.36 55
upstream ENSMUSE00000250716 Chr9:107689583..107689729 GAAGTCTATGTGCCCCAGGA Chr9:107689707..107689726 60.07 55
upstream ENSMUSE00000250692 Chr9:107686021..107686116 No primer for this exon
upstream ENSMUSE00000250672 Chr9:107684941..107685195 TCCTGGGTGAATATGGAGGA Chr9:107685148..107685167 60.27 50
upstream ENSMUSE00000250644 Chr9:107681905..107681979 AGCAAGAGCTCGCCTATCTG Chr9:107681923..107681942 59.88 55

*** Putative Vector Insertion (Chr 9: 107680359 - 107681904) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000250611 Chr9:107680261..107680358 CCCTTCGGTCATTTCCTTTT Chr9:107680303..107680322 60.29 45
downstream ENSMUSE00000250591 Chr9:107676923..107677052 TCCTCTGATGAACCCAATCC Chr9:107676902..107676921 59.86 50
downstream ENSMUSE00000389387 Chr9:107675896..107676138 CGAACAGCGTCTCGGTAAGT Chr9:107676028..107676047 60.45 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGAGCGGGAGGTAAGCTCT Chr9:107681894..107681914 60.12 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGAGGAGAGAGCGGGAGGTA Chr9:107681900..107681920 60.49 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032582