Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10346
Trapped Gene
Nedd4 (ENSMUSG00000032216)
Vector Insertion
Chr 9: 72590568 - 72591346
Public Clones XA209 (baygenomics)
Private Clones OST437392 (lexicon) OST21579 (lexicon) OST14636 (lexicon)
Severity of mutation (?) Insertion after 90% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000309593 (Chr9:72590460..72590567 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGGTCATCCACTGGTTCTGG Chr9:72590545..72590564 59.96 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000309593 (Chr9:72590460..72590567 +)
Downstram Exon
ENSMUSE00000217809 (Chr9:72591347..72591443 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGGTCATCCACTGGTTCTGG Chr9:72590545..72590564 59.96 55 TTTTTCCGAATCCATCATCC Chr9:72591376..72591395 59.7 40

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
upstream ENSMUSE00000311269 Chr9:72517759..72517923 TCACTGCTGATCCGTACCTG Chr9:72517892..72517911 59.85 55
upstream ENSMUSE00000406942 Chr9:72519037..72519110 ATAGGCCTGGCCAAGAAAGA Chr9:72519076..72519095 61.08 50
upstream ENSMUSE00000356446 Chr9:72525122..72525200 CTTACCAGCGTGCAGACAAA Chr9:72525168..72525187 60.05 50
upstream ENSMUSE00000311211 Chr9:72525300..72525338 No primer for this exon
upstream ENSMUSE00000311189 Chr9:72533868..72533921 CCGCATTCTTTTCGAAGTGT Chr9:72533885..72533904 60.25 45
upstream ENSMUSE00000217798 Chr9:72556919..72556969 AGGTCAAGTGGATGTCCCTCT Chr9:72556936..72556956 59.98 52.38
upstream ENSMUSE00000531958 Chr9:72558285..72558346 CCCAAGAATGGAGAGACCAT Chr9:72558293..72558312 58.94 50
upstream ENSMUSE00000217796 Chr9:72559974..72560073 CAGACCAGGCTGAGGAGTTAG Chr9:72560051..72560071 59.1 57.14
upstream ENSMUSE00000217781 Chr9:72566025..72566191 GGTTGTTTTGGACCAACCAG Chr9:72566033..72566052 60.25 50
upstream ENSMUSE00000217766 Chr9:72569108..72569225 ATATCGGAGGATGTGGATGG Chr9:72569181..72569200 59.59 50
upstream ENSMUSE00000217811 Chr9:72569304..72569468 GTGCAGACTCACCTTGCAGA Chr9:72569385..72569404 60.19 55
upstream ENSMUSE00000217808 Chr9:72572824..72572889 GGCAGCTTGCAGACCTGTAT Chr9:72572842..72572861 60.43 55
upstream ENSMUSE00000217764 Chr9:72574218..72574337 AAAACCACCACATGGTCCAA Chr9:72574305..72574324 61.06 45
upstream ENSMUSE00000217794 Chr9:72578709..72578780 AGATCGAAAATCCCTGCTCA Chr9:72578718..72578737 59.77 45
upstream ENSMUSE00000217762 Chr9:72579029..72579083 CAGATGGGCGAGTCTTCTTC Chr9:72579054..72579073 59.95 55
upstream ENSMUSE00000217773 Chr9:72579185..72579243 AAGACCCAGTGGGAAGATCC Chr9:72579193..72579212 60.31 55
upstream ENSMUSE00000217792 Chr9:72580399..72580464 GCAGTGCCCTACTCCAGAGA Chr9:72580399..72580418 60.56 60
upstream ENSMUSE00000217760 Chr9:72582817..72583046 CCCTTACTACGGCCTGTTTG Chr9:72583014..72583033 59.63 55
upstream ENSMUSE00000217790 Chr9:72584474..72584595 GGGATGGCAGTTTATCATGG Chr9:72584562..72584581 60.15 50
upstream ENSMUSE00000493621 Chr9:72584681..72584751 TTTCATCCGTCCGTTTTACA Chr9:72584685..72584704 59.01 40
upstream ENSMUSE00000309688 Chr9:72586847..72586942 TCTCTGCGATGGATTCTTGA Chr9:72586865..72586884 59.48 45
upstream ENSMUSE00000217775 Chr9:72587262..72587335 TGAAAACCGGAGGATCAGAG Chr9:72587278..72587297 60.19 50
upstream ENSMUSE00000217759 Chr9:72587975..72588035 GCGATTTGTGAACCGTATCC Chr9:72587990..72588009 60.34 50
upstream ENSMUSE00000531935 Chr9:72589435..72589494 No primer for this exon
upstream ENSMUSE00000309593 Chr9:72590460..72590567 AGGTCATCCACTGGTTCTGG Chr9:72590545..72590564 59.96 55

*** Putative Vector Insertion (Chr 9: 72590568 - 72591346) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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
  No PCR available

Come back to gene ENSMUSG00000032216