Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3028
Trapped Gene
Nedd4 (ENSMUSG00000032216)
Vector Insertion
Chr 9: 72510421 - 72517758
Public Clones XR0065 (sanger) (sanger) (sanger) XP0171 (sanger) (sanger)
(sanger) (sanger) RRT124 (baygenomics) XK121 (baygenomics) RRX136 (baygenomics)
(ggtc) H011F08 (ggtc) (ggtc) D178H01 (ggtc) (ggtc) M125D04 (ggtc)
(ggtc) E088E08 (ggtc) (ggtc) (ggtc) P010F02 (ggtc) (ggtc)
P106C09 (ggtc) D188H04 (ggtc) (ggtc) P106C09 (ggtc) CMHD-GT_341G3-3 (cmhd)
PST20521-NR (escells) PST456-1 (escells) PST19733-NR (escells) Ayu21-T269 (egtc)
IST14712B11 (tigm)
Private Clones OST440282 (lexicon) OST390730 (lexicon) OST218979 (lexicon) OST197545 (lexicon)
OST189895 (lexicon) OST165081 (lexicon) OST129173 (lexicon) OST123298 (lexicon)
OST62113 (lexicon) OST53614 (lexicon) OST40190 (lexicon) OST15574 (lexicon)
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000635601 (Chr9:72510364..72510420 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCAGTACTCTCGGAGGACGA Chr9:72510400..72510419 60.4 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000635601 (Chr9:72510364..72510420 +)
Downstram Exon
ENSMUSE00000311269 (Chr9:72517759..72517923 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCAGTACTCTCGGAGGACGA Chr9:72510400..72510419 60.4 60 CAGGTACGGATCAGCAGTGA Chr9:72517914..72517933 59.85 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000635601 Chr9:72510364..72510420 CCAGTACTCTCGGAGGACGA Chr9:72510400..72510419 60.4 60

*** Putative Vector Insertion (Chr 9: 72510421 - 72517758) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000311269 Chr9:72517759..72517923 CAGGTACGGATCAGCAGTGA Chr9:72517914..72517933 59.85 55
downstream ENSMUSE00000406942 Chr9:72519037..72519110 GGCTCCCAAGATGTCTTTCTT Chr9:72519110..72519130 59.71 47.62
downstream ENSMUSE00000356446 Chr9:72525122..72525200 TTTGTCTGCACGCTGGTAAG Chr9:72525190..72525209 60.05 50
downstream ENSMUSE00000311211 Chr9:72525300..72525338 No primer for this exon
downstream ENSMUSE00000311189 Chr9:72533868..72533921 TTCGAAAAGAATGCGGTGTC Chr9:72533903..72533922 61.15 45
downstream ENSMUSE00000217798 Chr9:72556919..72556969 AGAGGGACATCCACTTGACCT Chr9:72556958..72556978 59.98 52.38
downstream ENSMUSE00000531958 Chr9:72558285..72558346 No primer for this exon
downstream ENSMUSE00000217796 Chr9:72559974..72560073 AGCCTGGTCTGCATTTTCAT Chr9:72560064..72560083 59.7 45
downstream ENSMUSE00000217781 Chr9:72566025..72566191 GCATCTGGTTGGTCCAAAAC Chr9:72566059..72566078 60.36 50
downstream ENSMUSE00000217766 Chr9:72569108..72569225 CATTGTCTTCATCCGTGAGG Chr9:72569136..72569155 59.09 50
downstream ENSMUSE00000217811 Chr9:72569304..72569468 CTGGATTTCCACACACAGCA Chr9:72569445..72569464 60.72 50
downstream ENSMUSE00000217808 Chr9:72572824..72572889 No primer for this exon
downstream ENSMUSE00000217764 Chr9:72574218..72574337 GGTGGCAATCCAGATGAAGT Chr9:72574249..72574268 59.93 50
downstream ENSMUSE00000217794 Chr9:72578709..72578780 CAGGGATTTTCGATCTTGGA Chr9:72578736..72578755 60.01 45
downstream ENSMUSE00000217762 Chr9:72579029..72579083 GAAGAAGACTCGCCCATCTG Chr9:72579076..72579095 59.95 55
downstream ENSMUSE00000217773 Chr9:72579185..72579243 AGGATCTTCCCACTGGGTCT Chr9:72579216..72579235 59.93 55
downstream ENSMUSE00000217792 Chr9:72580399..72580464 No primer for this exon
downstream ENSMUSE00000217760 Chr9:72582817..72583046 CAGGCCGTAGTAAGGGTTGA Chr9:72583032..72583051 60.12 55
downstream ENSMUSE00000217790 Chr9:72584474..72584595 GCCATGATAAACTGCCATCC Chr9:72584585..72584604 60.3 50
downstream ENSMUSE00000493621 Chr9:72584681..72584751 GACTCCATGTCGTGCAGTGT Chr9:72584750..72584769 59.74 55
downstream ENSMUSE00000309688 Chr9:72586847..72586942 TCAAGAATCCATCGCAGAGA Chr9:72586887..72586906 59.48 45
downstream ENSMUSE00000217775 Chr9:72587262..72587335 CTCTGATCCTCCGGTTTTCA Chr9:72587300..72587319 60.19 50
downstream ENSMUSE00000217759 Chr9:72587975..72588035 TGGATACGGTTCACAAATCG Chr9:72588013..72588032 59.4 45
downstream ENSMUSE00000531935 Chr9:72589435..72589494 No primer for this exon
downstream ENSMUSE00000309593 Chr9:72590460..72590567 CCAGAACCAGTGGATGACCT Chr9:72590567..72590586 59.96 55
downstream ENSMUSE00000217809 Chr9:72591347..72591443 TTTTTCCGAATCCATCATCC Chr9:72591376..72591395 59.7 40
downstream ENSMUSE00000217813 Chr9:72594214..72594286 GCTCTTGGCAGCTTATCAGG Chr9:72594280..72594299 60.12 55
downstream ENSMUSE00000583984 Chr9:72594933..72597649 TCACATCCTGCCGTACACAT Chr9:72595269..72595288 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGATGTGTAATCGCCTTGCAG Chr9:72513465..72513486 60.28 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGAACAGATGTGCGTGACTG Chr9:72513460..72513480 59.43 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032216