Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31092
Trapped Gene
Tnrc6c (ENSMUSG00000025571)
Vector Insertion
Chr 11: 117516646 - 117562038
Public Clones (sanger) (sanger) (sanger) (sanger) 3SE289D01 (ggtc) 5SD183D09 (ggtc)
5SD034G02 (ggtc) 5SD172B02 (ggtc) 3SD032H11 (ggtc) 5SD069D03 (ggtc)
3SD176D10 (ggtc) 3SD034G02 (ggtc) 3SD172B02 (ggtc) 5SE044B05 (ggtc)
3SD069D03 (ggtc) 3SP134G03 (ggtc) 5SD032H11 (ggtc) IST14727G9 (tigm)
IST14790E12 (tigm) IST14653D6 (tigm) IST14451G2 (tigm) IST14766F11 (tigm)
IST14901E12 (tigm) IST14397E10 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000669544 (Chr11:117516127..117516645 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000669544 (Chr11:117516127..117516645 +)
Downstram Exon
ENSMUSE00000719540 (Chr11:117562039..117562138 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000669557 Chr11:117515603..117516000 CGGGTATTAGGGGAGAAGGA Chr11:117515884..117515903 60.27 55
upstream ENSMUSE00000669544 Chr11:117516127..117516645 No primer for this exon

*** Putative Vector Insertion (Chr 11: 117516646 - 117562038) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000588355 Chr11:117562039..117562138 No primer for this exon
downstream ENSMUSE00000719540 Chr11:117562039..117562138 No primer for this exon
downstream ENSMUSE00000669555 Chr11:117563693..117563714 No primer for this exon
downstream ENSMUSE00000585375 Chr11:117575440..117575766 GCTGCCGCTAGAAATAGTGC Chr11:117575531..117575550 60.15 55
downstream ENSMUSE00000369101 Chr11:117582264..117584864 GCTTATGAGCCCAGTTCTGC Chr11:117584495..117584514 59.99 55
downstream ENSMUSE00000387326 Chr11:117593482..117593694 CCAGGGTACAAGGGGAAGAT Chr11:117593568..117593587 60.18 55
downstream ENSMUSE00000246693 Chr11:117594924..117595090 GCAGGATGAGCTGCTTTCTT Chr11:117595054..117595073 59.72 50
downstream ENSMUSE00000377801 Chr11:117597286..117597366 GGAAGCCCATGTCTGTGAGT Chr11:117597367..117597386 60.12 55
downstream ENSMUSE00000246673 Chr11:117599605..117599662 GGCCTGGTCAAGGTTCATAC Chr11:117599661..117599680 59.41 55
downstream ENSMUSE00000246665 Chr11:117601181..117601323 TAGTCGGTCATTCCCAGTCC Chr11:117601241..117601260 59.93 55
downstream ENSMUSE00000363199 Chr11:117602959..117603132 GCCATCCTGATTGGAGAAAG Chr11:117602991..117603010 59.63 50
downstream ENSMUSE00000406457 Chr11:117604241..117604378 GGCTGGGAGGAATTAAGAGG Chr11:117604341..117604360 60.03 55
downstream ENSMUSE00000364572 Chr11:117608491..117608610 GAGCTGGTTCAACATCGTCA Chr11:117608598..117608617 59.84 50
downstream ENSMUSE00000151711 Chr11:117610558..117610641 CTGGGCCTGTAACATCTGCT Chr11:117610605..117610624 60.28 55
downstream ENSMUSE00000349816 Chr11:117610891..117611131 AGGTGTTGGGTGAAGACTGC Chr11:117611116..117611135 60.16 55
downstream ENSMUSE00000382209 Chr11:117614291..117614458 GGAGTTGGGATGTGTCCACT Chr11:117614406..117614425 59.82 55
downstream ENSMUSE00000151708 Chr11:117616645..117616836 TACCGGCCGTAAGAGTCATC Chr11:117616717..117616736 60.1 55
downstream ENSMUSE00000246537 Chr11:117617277..117617420 AGGTAGCGGTTGACATCCTG Chr11:117617409..117617428 60.13 55
downstream ENSMUSE00000408588 Chr11:117619251..117619445 TTCTGGGTACCTTCCACAGC Chr11:117619346..117619365 60.11 55
downstream ENSMUSE00000151706 Chr11:117620218..117620288 GAGCCAGCTGCTTGTTCTTC Chr11:117620267..117620286 60.28 55
downstream ENSMUSE00000575390 Chr11:117620938..117621077 CACAGCGTCCGAAGTGTAGA Chr11:117620969..117620988 60.05 55
downstream ENSMUSE00000401973 Chr11:117621805..117624751 ACGAAACGAGGGTAATGTGC Chr11:117622668..117622687 60 50
downstream ENSMUSE00000669543 Chr11:117621805..117624753 ACGAAACGAGGGTAATGTGC Chr11:117622668..117622687 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTTTGTTCGTAATCGCCTTG Chr11:117537688..117537708 58.44 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTTCCAAATGAGCCCAGAAA Chr11:117537635..117537655 60.05 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025571