Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI29343
Trapped Gene
Rbm42 (
ENSMUSG00000036733
)
Vector Insertion
Chr 7: 31426326 - 31429636
Public Clones
PSTVU01.HE33T (vanderbilt)
PSTVU01.E401 (vanderbilt)
Private Clones
not available
Severity of mutation
(?)
Insertion after 79% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000242772 (Chr7:31429518..31429635 -)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
AGCCACTGGGTGAAGACAAG
Chr7:31429609..31429628
60.3
55
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000242772 (Chr7:31429518..31429635 -)
Downstram Exon
ENSMUSE00000242765 (Chr7:31426327..31426521 -)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
AGCCACTGGGTGAAGACAAG
Chr7:31429609..31429628
60.3
55
GTTCACCTCATTGCCCAGAT
Chr7:31426456..31426475
59.93
50
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000242812
Chr7:31434957..31435184
AAAGAAATGGAGGCGGAGAT
Chr7:31434963..31434982
60.04
45
upstream
ENSMUSE00000675741
Chr7:31434957..31435163
AAAGAAATGGAGGCGGAGAT
Chr7:31434963..31434982
60.04
45
upstream
ENSMUSE00000675743
Chr7:31434957..31435336
AAAGAAATGGAGGCGGAGAT
Chr7:31434963..31434982
60.04
45
upstream
ENSMUSE00000242805
Chr7:31434603..31434738
CTGTGATCCGCCCAATTATC
Chr7:31434624..31434643
60.3
50
upstream
ENSMUSE00000242800
Chr7:31432750..31432834
TGCAGCCACAGTTGTTCCTC
Chr7:31432783..31432802
62.43
55
upstream
ENSMUSE00000242796
Chr7:31432579..31432653
ATCGTGGTCACCTGGACAGT
Chr7:31432616..31432635
60.44
55
upstream
ENSMUSE00000242791
Chr7:31430938..31431003
CCACGTGCTACAGAGAGCAG
Chr7:31430938..31430957
59.79
60
upstream
ENSMUSE00000242784
Chr7:31430686..31430861
GGGTTCTATGGCTGCTCTGA
Chr7:31430697..31430716
60.36
55
upstream
ENSMUSE00000675740
Chr7:31430686..31430840
GGGTTCTATGGCTGCTCTGA
Chr7:31430697..31430716
60.36
55
upstream
ENSMUSE00000242778
Chr7:31429845..31430177
GCTCTTGTCTCTCCGTCCAC
Chr7:31429895..31429914
59.99
60
upstream
ENSMUSE00000242772
Chr7:31429518..31429635
AGCCACTGGGTGAAGACAAG
Chr7:31429609..31429628
60.3
55
upstream
ENSMUSE00000242765
Chr7:31426327..31426521
AAGGCTAAGGTGATCCGTGA
Chr7:31426413..31426432
59.69
50
*** Putative Vector Insertion (Chr 7: 31426326 - 31429636) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000675744
Chr7:31426021..31426239
ATGCTTTTGCGAAGCTTGAT
Chr7:31426175..31426194
59.99
40
downstream
ENSMUSE00000412401
Chr7:31426018..31426239
ATGCTTTTGCGAAGCTTGAT
Chr7:31426175..31426194
59.99
40
downstream
ENSMUSE00000675742
Chr7:31426013..31426239
ATGCTTTTGCGAAGCTTGAT
Chr7:31426175..31426194
59.99
40
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
GGCCTAGAGAGTCCCAGAGG
Chr7:31426656..31426676
60.35
65
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
TAACCGTGACTGGGAAAACC
Chr7:31426569..31426589
59.83
50
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000036733