Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI11228
Trapped Gene
Sema4b (ENSMUSG00000030539)
Vector Insertion
Chr 7: 87365218 - 87365327
Public Clones G033C05 (ggtc) P076G08 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 55% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000200266 (Chr7:87365007..87365217 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCAGACCGAGTGCTGAACTT Chr7:87365058..87365077 60.44 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000200266 (Chr7:87365007..87365217 +)
Downstram Exon
ENSMUSE00000200270 (Chr7:87365328..87365443 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCAGACCGAGTGCTGAACTT Chr7:87365058..87365077 60.44 55 CTCTGGAGCTCAGGGTCACT Chr7:87365372..87365391 59.58 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000507158 Chr7:87331727..87331877 TTCACGGGATACTCCAGGTC Chr7:87331757..87331776 59.93 55
upstream ENSMUSE00000475341 Chr7:87343405..87343656 TTCCACTTGAGCAACCTGAG Chr7:87343470..87343489 59.01 50
upstream ENSMUSE00000718257 Chr7:87343405..87343656 TTCCACTTGAGCAACCTGAG Chr7:87343470..87343489 59.01 50
upstream ENSMUSE00000200269 Chr7:87357682..87357845 ATGGCAAGACGCTGTATGTG Chr7:87357757..87357776 59.75 50
upstream ENSMUSE00000200268 Chr7:87358149..87358211 CAGATGCTGACAGGAAGCAG Chr7:87358162..87358181 59.73 55
upstream ENSMUSE00000200275 Chr7:87360510..87360608 ATCCTCCTGCCACTCAACAG Chr7:87360534..87360553 60.26 55
upstream ENSMUSE00000200283 Chr7:87361215..87361326 ACTTCAAGTCCACGGCTCTG Chr7:87361300..87361319 60.44 55
upstream ENSMUSE00000317215 Chr7:87361616..87361729 CTGAGAGCTCCCTCAACTGG Chr7:87361703..87361722 60.13 60
upstream ENSMUSE00000317206 Chr7:87361834..87361985 AGCCCCATAGGTGATGATGA Chr7:87361878..87361897 60.3 50
upstream ENSMUSE00000200282 Chr7:87363769..87363950 GCGCAAGACCCTTTTCTATG Chr7:87363912..87363931 59.85 50
upstream ENSMUSE00000200267 Chr7:87364072..87364222 TTGACGGCCTGTACAAGAAA Chr7:87364137..87364156 59.32 45
upstream ENSMUSE00000200266 Chr7:87365007..87365217 CCAGACCGAGTGCTGAACTT Chr7:87365058..87365077 60.44 55

*** Putative Vector Insertion (Chr 7: 87365218 - 87365327) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000200270 Chr7:87365328..87365443 CTCTGGAGCTCAGGGTCACT Chr7:87365372..87365391 59.58 60
downstream ENSMUSE00000200274 Chr7:87365674..87365840 GAATGGGAGGAGGCATACAA Chr7:87365702..87365721 59.89 50
downstream ENSMUSE00000672952 Chr7:87365674..87366718 GCCAGATCAGGCTGGTAGAG Chr7:87365837..87365856 59.97 60
downstream ENSMUSE00000317179 Chr7:87368820..87368902 AAGAAACCGGGCCTTGTATG Chr7:87368898..87368917 61.22 50
downstream ENSMUSE00000406768 Chr7:87369482..87371410 GATTCTCAACTTCGGCTTGC Chr7:87370599..87370618 59.96 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TACATGCATAATCGCCTTGC Chr7:87365261..87365281 59.69 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAGGAGGGCAATACATGCAC Chr7:87365250..87365270 59.96 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030539