Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI24295
Trapped Gene
Nipsnap1 (ENSMUSG00000034285)
Vector Insertion
Chr 11: 4784120 - 4788882
Public Clones IST11324F5 (tigm)
Private Clones OST225522 (lexicon)
Severity of mutation (?) Insertion after 49% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000307918 (Chr11:4784025..4784119 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACTATCCCTGCTCGCTTGTG Chr11:4784060..4784079 60.42 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000307918 (Chr11:4784025..4784119 +)
Downstram Exon
ENSMUSE00000307909 (Chr11:4788883..4788953 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACTATCCCTGCTCGCTTGTG Chr11:4784060..4784079 60.42 55 CTGAGAACCGCCATAGGTGT Chr11:4788906..4788925 60.13 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000406462 Chr11:4774006..4774106 GCTATTCACGAAGCCGAGAC Chr11:4774050..4774069 59.99 55
upstream ENSMUSE00000581372 Chr11:4782972..4783174 CGTGTCCATTCAGAGCAAAG Chr11:4783066..4783085 59.44 50
upstream ENSMUSE00000581370 Chr11:4783222..4783256 TTGCTTAGGAAGCTCCTGCT Chr11:4783230..4783249 59.36 50
upstream ENSMUSE00000307937 Chr11:4783371..4783498 CACTCCACTCTGCTGTCCAA Chr11:4783447..4783466 60.02 55
upstream ENSMUSE00000307927 Chr11:4783729..4783774 CCGAATGTCTGGATGCCTAC Chr11:4783744..4783763 60.48 55
upstream ENSMUSE00000307918 Chr11:4784025..4784119 ACTATCCCTGCTCGCTTGTG Chr11:4784060..4784079 60.42 55

*** Putative Vector Insertion (Chr 11: 4784120 - 4788882) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000307909 Chr11:4788883..4788953 CTGAGAACCGCCATAGGTGT Chr11:4788906..4788925 60.13 55
downstream ENSMUSE00000715271 Chr11:4789100..4789240 ACTGGTTTCTCCTGGACAGC Chr11:4789160..4789179 59.31 55
downstream ENSMUSE00000718600 Chr11:4789100..4789240 ACTGGTTTCTCCTGGACAGC Chr11:4789160..4789179 59.31 55
downstream ENSMUSE00000656061 Chr11:4789536..4789567 CCCATTCAATCATGGTTCCT Chr11:4789560..4789579 59.6 45
downstream ENSMUSE00000656070 Chr11:4789536..4789567 CCCATTCAATCATGGTTCCT Chr11:4789560..4789579 59.6 45
downstream ENSMUSE00000656058 Chr11:4789895..4789989 TCTCCTGACGGTACTTGATGG Chr11:4789925..4789945 60.12 52.38
downstream ENSMUSE00000656069 Chr11:4789895..4789989 TCTCCTGACGGTACTTGATGG Chr11:4789925..4789945 60.12 52.38
downstream ENSMUSE00000656056 Chr11:4791406..4791489 TTCGAGTCTCCTCCCGAGAT Chr11:4791444..4791463 61.27 55
downstream ENSMUSE00000656068 Chr11:4791406..4791489 TTCGAGTCTCCTCCCGAGAT Chr11:4791444..4791463 61.27 55
downstream ENSMUSE00000307866 Chr11:4793123..4794203 TTGTCGAAGCTGAACACCAC Chr11:4793321..4793340 59.88 50
downstream ENSMUSE00000595105 Chr11:4793123..4794203 TTGTCGAAGCTGAACACCAC Chr11:4793321..4793340 59.88 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATCGCCTTGCAGCACATC Chr11:4787171..4787191 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGCCTTTGTCTCCGTGACT Chr11:4787158..4787178 60.44 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034285