Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6350
Trapped Gene
Rbbp4 (ENSMUSG00000057236)
Vector Insertion
Chr 4: 129005978 - 129011740
Public Clones YHC246 (baygenomics) IST10083F7 (tigm) IST10083F8 (tigm) IST10083E7 (tigm)
Private Clones OST244184 (lexicon) OST177544 (lexicon) OST62237 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000662047 (Chr4:129011741..129011888 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAGAACGGGTGATCAACGAG Chr4:129011848..129011867 60.11 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000662047 (Chr4:129011741..129011888 -)
Downstram Exon
ENSMUSE00000474672 (Chr4:129005832..129005977 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAGAACGGGTGATCAACGAG Chr4:129011848..129011867 60.11 50 AAGCCGATGAATGCTGAAAT Chr4:129005922..129005941 59.67 40

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

*** Putative Vector Insertion (Chr 4: 129005978 - 129011740) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000474672 Chr4:129005832..129005977 AAGCCGATGAATGCTGAAAT Chr4:129005922..129005941 59.67 40
downstream ENSMUSE00000182353 Chr4:128999940..129000113 AATGATGCAGGGGTTCTGAG Chr4:128999982..129000001 60.07 50
downstream ENSMUSE00000182364 Chr4:128999597..128999712 AAGTGCCCACTGAGATTTGG Chr4:128999597..128999616 60.11 50
downstream ENSMUSE00000182362 Chr4:128999323..128999483 GTCTTTGCATCCACCACCTT Chr4:128999400..128999419 59.97 50
downstream ENSMUSE00000411932 Chr4:128999098..128999224 TGTGTGAGCATCAACCGAGT Chr4:128999145..128999164 60.32 50
downstream ENSMUSE00000364055 Chr4:128997713..128997790 GGGATTCAAAGGAGTGCAAC Chr4:128997711..128997730 59.53 50
downstream ENSMUSE00000182356 Chr4:128995688..128995764 ACGATCGGTACCACTGGAAG Chr4:128995689..128995708 59.99 55
downstream ENSMUSE00000182368 Chr4:128995106..128995163 CATCTTCTGGGGACTGCTCT Chr4:128995110..128995129 59.4 55
downstream ENSMUSE00000467517 Chr4:128994892..128995002 AACAAATCACCCAAGGCTCA Chr4:128994908..128994927 60.49 45
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 TAATCGCCTTGCAGCACATC Chr4:129011669..129011689 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATAATCGCCTTGCAGCACAT Chr4:129005819..129005839 60.64 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 3 ACCTGGTGATTGCCAGTGTC Chr4:129008888..129008908 61 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000057236