Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4245
Trapped Gene
Rbbp4 (ENSMUSG00000057236)
Vector Insertion
Chr 4: 128987402 - 128994891
Public Clones AD0773 (sanger) AK0124 (sanger) RRS676 (baygenomics) CMHD-GT_451G8-3 (cmhd)
Private Clones OST436528 (lexicon) OST360787 (lexicon) OST42389 (lexicon) OST19868 (lexicon)
Severity of mutation (?) Insertion after 95% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000467517 (Chr4:128994892..128995002 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AATGAGCCTTGGGTGATTTG Chr4:128994932..128994951 59.93 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000467517 (Chr4:128994892..128995002 -)
Downstram Exon
ENSMUSE00000662046 (Chr4:128986762..128987401 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AATGAGCCTTGGGTGATTTG Chr4:128994932..128994951 59.93 45 GGGCTTGTAGCATTGTTGGT Chr4:128987180..128987199 60 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000662048 Chr4:129012462..129012584 No primer for this exon
upstream ENSMUSE00000662047 Chr4:129011741..129011888 AAGAACGGGTGATCAACGAG Chr4:129011848..129011867 60.11 50
upstream ENSMUSE00000474672 Chr4:129005832..129005977 CCAGTGTCCAGCTCCCTAAT Chr4:129005878..129005897 59.16 55
upstream ENSMUSE00000182353 Chr4:128999940..129000113 CTCAGAACCCCTGCATCATT Chr4:129000004..129000023 60.07 50
upstream ENSMUSE00000182364 Chr4:128999597..128999712 ACCCTTCTGGAGAATGCAAC Chr4:128999693..128999712 59.14 50
upstream ENSMUSE00000182362 Chr4:128999323..128999483 AAGGTGGTGGATGCAAAGAC Chr4:128999422..128999441 59.97 50
upstream ENSMUSE00000411932 Chr4:128999098..128999224 ACTCGGTTGATGCTCACACA Chr4:128999167..128999186 60.32 50
upstream ENSMUSE00000364055 Chr4:128997713..128997790 TTGTGGGATCTGAGGAATCTG Chr4:128997761..128997781 60.06 47.62
upstream ENSMUSE00000182356 Chr4:128995688..128995764 GGTACCGATCGTAGGCTGAA Chr4:128995703..128995722 60.1 55
upstream ENSMUSE00000182368 Chr4:128995106..128995163 GAAGAGCAGTCCCCAGAAGA Chr4:128995134..128995153 59.53 55
upstream ENSMUSE00000467517 Chr4:128994892..128995002 AATGAGCCTTGGGTGATTTG Chr4:128994932..128994951 59.93 45

*** Putative Vector Insertion (Chr 4: 128987402 - 128994891) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000662046 Chr4:128986762..128987401 GGGCTTGTAGCATTGTTGGT Chr4:128987180..128987199 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGGTTCAACCGTCAGCTTTG Chr4:128994899..128994919 60.29 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGGTTCAACCGTCAGCTTTG Chr4:128994899..128994919 60.29 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000057236