Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25742
Trapped Gene
Nrip1 (ENSMUSG00000048490)
Vector Insertion
Chr 16: 76295261 - 76330990
Public Clones E114B06 (ggtc) (ggtc) D095A08 (ggtc) IST12543G12 (tigm) IST11630G4 (tigm)
IST15050A4 (tigm) IST15050A3 (tigm)
Private Clones OST168339 (lexicon) OST86843 (lexicon) OST65548 (lexicon) OST33243 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000389637 (Chr16:76330991..76331109 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAACAGCCTTCTCAGCTTCC Chr16:76331027..76331046 60.13 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000389637 (Chr16:76330991..76331109 -)
Downstram Exon
ENSMUSE00000348925 (Chr16:76291107..76295260 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAACAGCCTTCTCAGCTTCC Chr16:76331027..76331046 60.13 55 GTTGTGGGTCTGGAAGTCGT Chr16:76292587..76292606 60.01 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000719562 Chr16:76374015..76374072 AGGGAGCTAGCTGTGCACTC Chr16:76374020..76374039 59.78 60
upstream ENSMUSE00000406006 Chr16:76373117..76373294 ACGGCTAACCTGGGAAGGAG Chr16:76373158..76373177 62.76 60
upstream ENSMUSE00000357001 Chr16:76352717..76352794 ACATTCGGGAGGAACACATC Chr16:76352723..76352742 59.79 50
upstream ENSMUSE00000719682 Chr16:76352717..76352791 ACATTCGGGAGGAACACATC Chr16:76352723..76352742 59.79 50
upstream ENSMUSE00000389637 Chr16:76330991..76331109 CAACAGCCTTCTCAGCTTCC Chr16:76331027..76331046 60.13 55

*** Putative Vector Insertion (Chr 16: 76295261 - 76330990) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000348925 Chr16:76291107..76295260 GTTGTGGGTCTGGAAGTCGT Chr16:76292587..76292606 60.01 55
downstream ENSMUSE00000714196 Chr16:76287645..76295260 ACTGTCGTGTTGGATGACCA Chr16:76288363..76288382 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGCTTCAGCATTCAGCCTA Chr16:76300937..76300957 59.32 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGATGCAGCTCAAGGTCACT Chr16:76301010..76301030 59.58 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CTCTGTAACCGCCCTCGTAA Chr16:76301137..76301157 60.26 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CTCTGTAACCGCCCTCGTAA Chr16:76301137..76301157 60.26 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048490