Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI17399
Trapped Gene
Usp12 (ENSMUSG00000029640)
Vector Insertion
Chr 5: 147580594 - 147606190
Public Clones (sanger) (sanger) (ggtc) IST13599G1 (tigm) IST14186H11 (tigm)
Private Clones OST443461 (lexicon) OST349253 (lexicon) OST308913 (lexicon) OST250763 (lexicon)
OST233568 (lexicon) OST167779 (lexicon) OST136611 (lexicon) OST46996 (lexicon)
Severity of mutation (?) Insertion after 4% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000714055 (Chr5:147606191..147606532 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTCGCCTCCATCTGTACCAT Chr5:147606192..147606211 60.48 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000714055 (Chr5:147606191..147606532 -)
Downstram Exon
ENSMUSE00000376315 (Chr5:147580513..147580593 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTCGCCTCCATCTGTACCAT Chr5:147606192..147606211 60.48 50 CCAAAATAGTGCTCGTTGACC Chr5:147580501..147580521 59.62 47.62

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000711990 Chr5:147606191..147606532 TTCGCCTCCATCTGTACCAT Chr5:147606192..147606211 60.48 50
upstream ENSMUSE00000714055 Chr5:147606191..147606532 TTCGCCTCCATCTGTACCAT Chr5:147606192..147606211 60.48 50

*** Putative Vector Insertion (Chr 5: 147580594 - 147606190) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000376315 Chr5:147580513..147580593 CCAAAATAGTGCTCGTTGACC Chr5:147580501..147580521 59.62 47.62
downstream ENSMUSE00000589481 Chr5:147580513..147580593 CGTTGACCGGAAACTGTTCT Chr5:147580514..147580533 60.15 50
downstream ENSMUSE00000263651 Chr5:147574777..147574990 CCGAAATGGACGACAAAAAT Chr5:147574906..147574925 59.8 40
downstream ENSMUSE00000486429 Chr5:147574777..147574990 CCGAAATGGACGACAAAAAT Chr5:147574906..147574925 59.8 40
downstream ENSMUSE00000190971 Chr5:147565946..147566175 CCCTGAAAGATCTCGTGGAC Chr5:147565964..147565983 59.65 55
downstream ENSMUSE00000589480 Chr5:147565946..147566175 CCCTGAAAGATCTCGTGGAC Chr5:147565964..147565983 59.65 55
downstream ENSMUSE00000647754 Chr5:147563469..147563545 TGTGTTTTGTTCCACGTCAA Chr5:147563467..147563486 58.57 40
downstream ENSMUSE00000647753 Chr5:147563271..147563354 CTCCGGCACTCTTCACAGTA Chr5:147563270..147563289 59.03 55
downstream ENSMUSE00000533711 Chr5:147551878..147552067 GCATCTCCTGACGTGTTGAA Chr5:147551902..147551921 59.84 50
downstream ENSMUSE00000263626 Chr5:147551870..147552067 GCATCTCCTGACGTGTTGAA Chr5:147551902..147551921 59.84 50
downstream ENSMUSE00000647752 Chr5:147551870..147551875 No primer for this exon
downstream ENSMUSE00000533709 Chr5:147550676..147550754 AATATAATGGCCTCGGTTGG Chr5:147550708..147550727 58.78 45
downstream ENSMUSE00000533718 Chr5:147550676..147550754 AATATAATGGCCTCGGTTGG Chr5:147550708..147550727 58.78 45
downstream ENSMUSE00000510269 Chr5:147546388..147549356 AACGACAATCCCCTGAAGTG Chr5:147547013..147547032 59.97 50
downstream ENSMUSE00000647751 Chr5:147546388..147549356 AACGACAATCCCCTGAAGTG Chr5:147547013..147547032 59.97 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCCTGTCGCCTCTGTTCTTT Chr5:147606167..147606187 59.99 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCTCAGAGAGTGCGTGACTG Chr5:147606131..147606151 59.92 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 ATGCCATTTGATTGGAGCAT Chr5:147582530..147582550 60.3 40 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 ATGCCATTTGATTGGAGCAT Chr5:147582530..147582550 60.3 40 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029640