Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5463
Trapped Gene
Setd8 (ENSMUSG00000049327)
Vector Insertion
Chr 5: 124897380 - 124900669
Public Clones CSJ210 (baygenomics) RRB075 (baygenomics) F062C06 (ggtc) CMHD-GT_305D01-3 (cmhd)
CMHD-GT_481E10-3 (cmhd)
Private Clones OST399065 (lexicon) OST82993 (lexicon) OST60642 (lexicon)
Severity of mutation (?) Insertion after 27% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000384855 (Chr5:124897223..124897379 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCCTACATGAGTCCGAACA Chr5:124897255..124897274 60.26 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000384855 (Chr5:124897223..124897379 +)
Downstram Exon
ENSMUSE00000322583 (Chr5:124900670..124900889 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCCTACATGAGTCCGAACA Chr5:124897255..124897274 60.26 50 TTCTGCTGCTTCGGATTTTT Chr5:124900791..124900810 59.96 40

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000426884 Chr5:124889939..124890024 No primer for this exon
upstream ENSMUSE00000687910 Chr5:124895502..124895737 No primer for this exon
upstream ENSMUSE00000649613 Chr5:124895548..124895583 No primer for this exon
upstream ENSMUSE00000649612 Chr5:124895586..124895672 No primer for this exon
upstream ENSMUSE00000649611 Chr5:124895675..124895737 No primer for this exon
upstream ENSMUSE00000398617 Chr5:124895978..124896093 No primer for this exon
upstream ENSMUSE00000384855 Chr5:124897223..124897379 TGCCTACATGAGTCCGAACA Chr5:124897255..124897274 60.26 50

*** Putative Vector Insertion (Chr 5: 124897380 - 124900669) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000322583 Chr5:124900670..124900889 TTCTGCTGCTTCGGATTTTT Chr5:124900791..124900810 59.96 40
downstream ENSMUSE00000322577 Chr5:124901295..124901382 CTCCGCACAGGGTAGAAATC Chr5:124901354..124901373 59.69 55
downstream ENSMUSE00000322573 Chr5:124907068..124907127 CTTCCTTCCCGCTCTCAATC Chr5:124907119..124907138 61.23 55
downstream ENSMUSE00000322569 Chr5:124909784..124909974 ACTGCTTGGTAGCGATCACA Chr5:124909835..124909854 59.47 50
downstream ENSMUSE00000687911 Chr5:124910496..124910550 CTAGGCGGTTCGTTTCTTGA Chr5:124910531..124910550 60.38 50
downstream ENSMUSE00000351091 Chr5:124910497..124912316 CTTCGGTCCCCATAGTCGTA Chr5:124910670..124910689 59.95 55
downstream ENSMUSE00000649608 Chr5:124910497..124910892 GTGTGTGTGTGTGCGTGTGT Chr5:124910816..124910835 60.18 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CGGCCTCATTATTCTGCTTT Chr5:124897393..124897413 59.32 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGGCCTCATTATTCTGCTTT Chr5:124897393..124897413 59.32 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000049327