Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28114
Trapped Gene
Samd4b (ENSMUSG00000037513)
Vector Insertion
Chr 7: 29193195 - 29198890
Public Clones not available
Private Clones OST39636 (lexicon)
Severity of mutation (?) Insertion after 32% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000254387 (Chr7:29198891..29199361 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TATTGGGAGCAATGCAAACA Chr7:29198894..29198913 60.07 40 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000254387 (Chr7:29198891..29199361 -)
Downstram Exon
ENSMUSE00000254399 (Chr7:29192955..29193194 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TATTGGGAGCAATGCAAACA Chr7:29198894..29198913 60.07 40 GGCTCGTAGGGATGAGTGAC Chr7:29193110..29193129 59.69 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000464193 Chr7:29208455..29208857 ATCCTCGCTAGCTGGTTCAA Chr7:29208607..29208626 59.98 50
upstream ENSMUSE00000254387 Chr7:29198891..29199361 TATTGGGAGCAATGCAAACA Chr7:29198894..29198913 60.07 40

*** Putative Vector Insertion (Chr 7: 29193195 - 29198890) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000254399 Chr7:29192955..29193194 GGCTCGTAGGGATGAGTGAC Chr7:29193110..29193129 59.69 60
downstream ENSMUSE00000254467 Chr7:29192488..29192597 CTGCGACTCTAGGTGCTGCT Chr7:29192466..29192485 60.9 60
downstream ENSMUSE00000254458 Chr7:29192250..29192336 GGACTTGAGGACGCTCTGTC Chr7:29192237..29192256 59.99 60
downstream ENSMUSE00000254452 Chr7:29191388..29191706 GACCCTCATCCTTGGCAGTA Chr7:29191567..29191586 60.07 55
downstream ENSMUSE00000254442 Chr7:29190973..29191058 CTTTTCGATGAGCTGGAGGT Chr7:29190966..29190985 59.43 50
downstream ENSMUSE00000254432 Chr7:29190508..29190626 GAATGTCCGGAGGAGTTTCA Chr7:29190533..29190552 60.05 50
downstream ENSMUSE00000254423 Chr7:29188883..29189081 GGCATGTCGAGGAGAGACAC Chr7:29188897..29188916 60.84 60
downstream ENSMUSE00000254416 Chr7:29188639..29188762 TGAGAATAGCCTGGGGTGAC Chr7:29188629..29188648 60.07 55
downstream ENSMUSE00000254413 Chr7:29186843..29186926 AAGGCGTGTTCTGTCATGCT Chr7:29186826..29186845 60.87 50
downstream ENSMUSE00000535275 Chr7:29185319..29186636 GGGTGGGAAAGTTTGACAGA Chr7:29185634..29185653 59.94 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATTGGGAGCAATGCAAACAC Chr7:29195891..29195911 60.9 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATTGGGAGCAATGCAAACAC Chr7:29195891..29195911 60.9 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037513