Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI11284
Trapped Gene
Sema4b (
ENSMUSG00000030539
)
Vector Insertion
Chr 7: 87365444 - 87365673
Public Clones
D004A01 (ggtc)
G074D03 (ggtc)
IST10677A4 (tigm)
IST10677A4 (tigm)
Private Clones
not available
Severity of mutation
(?)
Insertion after 60% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000200270 (Chr7:87365328..87365443 +)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
TCCACATCATTGAGGAGCTG
Chr7:87365370..87365389
59.79
50
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000200270 (Chr7:87365328..87365443 +)
Downstram Exon
ENSMUSE00000200274 (Chr7:87365674..87365840 +)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
TCCACATCATTGAGGAGCTG
Chr7:87365370..87365389
59.79
50
GAATGGGAGGAGGCATACAA
Chr7:87365702..87365721
59.89
50
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
upstream
ENSMUSE00000200270
Chr7:87365328..87365443
TCCACATCATTGAGGAGCTG
Chr7:87365370..87365389
59.79
50
*** Putative Vector Insertion (Chr 7: 87365444 - 87365673) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
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
AAGGACAGCCTGTGCAGAAC
Chr7:87365404..87365424
60.45
55
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
AAGGACAGCCTGTGCAGAAC
Chr7:87365404..87365424
60.45
55
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000030539