Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI1514
Trapped Gene
Etl4 (
ENSMUSG00000036617
)
Vector Insertion
Chr 2: 20583524 - 20583724
Public Clones
AC0642 (sanger)
CC0680 (sanger)
AT0343 (sanger)
TEA044 (baygenomics)
CSG442 (baygenomics)
TEA028 (baygenomics)
A055F05 (ggtc)
W064F06 (ggtc)
W064E06 (ggtc)
Private Clones
not available
Severity of mutation
(?)
Insertion after 0% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000717687 (Chr2:20583525..20583723 +)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
CCATGTCCGAGGGAGAAGTA
Chr2:20583619..20583638
60.06
55
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000717687 (Chr2:20583525..20583723 +)
Downstram Exon
ENSMUSE00000699932 (Chr2:20583525..20583723 +)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
CCATGTCCGAGGGAGAAGTA
Chr2:20583619..20583638
60.06
55
TACTTCTCCCTCGGACATGG
Chr2:20583641..20583660
60.06
55
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000699940
Chr2:19831407..19831906
CTCTTGCCACCGAAAGACTC
Chr2:19831746..19831765
59.99
55
upstream
ENSMUSE00000699939
Chr2:20038600..20038680
CTGGACCCTGTGTTTGACATC
Chr2:20038610..20038630
60.42
52.38
upstream
ENSMUSE00000699938
Chr2:20211521..20211668
AAAGTCGCCCTCAAAGGATT
Chr2:20211603..20211622
60.07
45
upstream
ENSMUSE00000699998
Chr2:20211540..20211668
AAAGTCGCCCTCAAAGGATT
Chr2:20211603..20211622
60.07
45
upstream
ENSMUSE00000699971
Chr2:20261523..20261736
AGAAGAAAACCAGCCGAGGT
Chr2:20261614..20261633
60.25
50
upstream
ENSMUSE00000699995
Chr2:20261549..20261736
AGAAGAAAACCAGCCGAGGT
Chr2:20261614..20261633
60.25
50
upstream
ENSMUSE00000410886
Chr2:20431674..20431886
TTGGCAACCTGAAGAACACA
Chr2:20431841..20431860
60.28
45
upstream
ENSMUSE00000708489
Chr2:20441140..20441554
AGAAATGTGAGCCGAACCTG
Chr2:20441504..20441523
60.26
50
upstream
ENSMUSE00000717316
Chr2:20441140..20441554
AGAAATGTGAGCCGAACCTG
Chr2:20441504..20441523
60.26
50
upstream
ENSMUSE00000721391
Chr2:20441140..20441554
AGAAATGTGAGCCGAACCTG
Chr2:20441504..20441523
60.26
50
upstream
ENSMUSE00000647336
Chr2:20441455..20441554
AGAAATGTGAGCCGAACCTG
Chr2:20441504..20441523
60.26
50
upstream
ENSMUSE00000423589
Chr2:20451586..20451869
CAGGGAACGCCTTTCTAATG
Chr2:20451644..20451663
59.7
50
upstream
ENSMUSE00000715347
Chr2:20451586..20451869
CAGGGAACGCCTTTCTAATG
Chr2:20451644..20451663
59.7
50
upstream
ENSMUSE00000716425
Chr2:20451586..20451869
CAGGGAACGCCTTTCTAATG
Chr2:20451644..20451663
59.7
50
*** Putative Vector Insertion (Chr 2: 20583524 - 20583724) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000699932
Chr2:20583525..20583723
TACTTCTCCCTCGGACATGG
Chr2:20583641..20583660
60.06
55
downstream
ENSMUSE00000713171
Chr2:20583525..20583723
TACTTCTCCCTCGGACATGG
Chr2:20583641..20583660
60.06
55
downstream
ENSMUSE00000717687
Chr2:20583525..20583723
TACTTCTCCCTCGGACATGG
Chr2:20583641..20583660
60.06
55
downstream
ENSMUSE00000410192
Chr2:20631032..20631230
GGAAAGGCACTGACGAAGAG
Chr2:20631137..20631156
59.99
55
downstream
ENSMUSE00000699967
Chr2:20631032..20631230
GGAAAGGCACTGACGAAGAG
Chr2:20631137..20631156
59.99
55
downstream
ENSMUSE00000272760
Chr2:20634982..20635075
GGCTTTCGTCATGTGGTTAAA
Chr2:20635059..20635079
59.99
42.86
downstream
ENSMUSE00000699966
Chr2:20634982..20635075
GGCTTTCGTCATGTGGTTAAA
Chr2:20635059..20635079
59.99
42.86
downstream
ENSMUSE00000699927
Chr2:20644252..20644350
TTCCAGACTCGCAGAGACCT
Chr2:20644314..20644333
60.13
55
downstream
ENSMUSE00000699929
Chr2:20658941..20659182
TTTGTTTTGACCCGGTCTTC
Chr2:20658985..20659004
59.95
45
downstream
ENSMUSE00000647337
Chr2:20665086..20665918
TGTCTTCATCCGGTTTGACA
Chr2:20665377..20665396
60.09
45
downstream
ENSMUSE00000699935
Chr2:20665086..20666443
ACCTGAACCCACTCATCCAG
Chr2:20666064..20666083
59.96
55
downstream
ENSMUSE00000709622
Chr2:20665086..20665918
TGTCTTCATCCGGTTTGACA
Chr2:20665377..20665396
60.09
45
downstream
ENSMUSE00000712334
Chr2:20665086..20665918
TGTCTTCATCCGGTTTGACA
Chr2:20665377..20665396
60.09
45
downstream
ENSMUSE00000647335
Chr2:20681174..20681278
CTGGCAATCTGCTTCTCCAT
Chr2:20681212..20681231
60.36
50
downstream
ENSMUSE00000423086
Chr2:20681842..20681891
GCTGTGGCTTTCACCATTTT
Chr2:20681868..20681887
60.12
45
downstream
ENSMUSE00000699964
Chr2:20681842..20681891
GCTGTGGCTTTCACCATTTT
Chr2:20681868..20681887
60.12
45
downstream
ENSMUSE00000423066
Chr2:20688072..20688238
TGTCAAGCAGGCTAGTGTGG
Chr2:20688185..20688204
60.05
55
downstream
ENSMUSE00000699963
Chr2:20688072..20688238
TGTCAAGCAGGCTAGTGTGG
Chr2:20688185..20688204
60.05
55
downstream
ENSMUSE00000699924
Chr2:20688199..20688238
TGGAGTTGGAGCCTGAGTTC
Chr2:20688222..20688241
60.39
55
downstream
ENSMUSE00000423064
Chr2:20699653..20699828
ACAATCCGCTCTTCTTCGTG
Chr2:20699819..20699838
60.4
50
downstream
ENSMUSE00000699962
Chr2:20699653..20699828
ACAATCCGCTCTTCTTCGTG
Chr2:20699819..20699838
60.4
50
downstream
ENSMUSE00000423061
Chr2:20702569..20702699
ACTCTGCCAGTGGAGGAAGA
Chr2:20702628..20702647
59.99
55
downstream
ENSMUSE00000699959
Chr2:20702569..20702699
ACTCTGCCAGTGGAGGAAGA
Chr2:20702628..20702647
59.99
55
downstream
ENSMUSE00000423058
Chr2:20703425..20703572
CAACTTCTATGCGCAGGACA
Chr2:20703481..20703500
60.01
50
downstream
ENSMUSE00000699958
Chr2:20703425..20703572
CAACTTCTATGCGCAGGACA
Chr2:20703481..20703500
60.01
50
downstream
ENSMUSE00000383856
Chr2:20706671..20707127
ACCATTCACTGGGGTCTGAG
Chr2:20707058..20707077
59.96
55
downstream
ENSMUSE00000699923
Chr2:20706671..20707127
ACCATTCACTGGGGTCTGAG
Chr2:20707058..20707077
59.96
55
downstream
ENSMUSE00000699944
Chr2:20706671..20707094
ACCATTCACTGGGGTCTGAG
Chr2:20707058..20707077
59.96
55
downstream
ENSMUSE00000699957
Chr2:20706671..20706862
GATAGGGGCACCACTTCTGA
Chr2:20706859..20706878
60.07
55
downstream
ENSMUSE00000272689
Chr2:20710055..20710238
GCATCTCCCTTTGACACTGG
Chr2:20710215..20710234
60.66
55
downstream
ENSMUSE00000699919
Chr2:20710055..20710238
GCATCTCCCTTTGACACTGG
Chr2:20710215..20710234
60.66
55
downstream
ENSMUSE00000272683
Chr2:20719504..20719658
AGACCACATCGCCTGATCTC
Chr2:20719638..20719657
60.23
55
downstream
ENSMUSE00000647334
Chr2:20719504..20719658
AGACCACATCGCCTGATCTC
Chr2:20719638..20719657
60.23
55
downstream
ENSMUSE00000343104
Chr2:20720243..20720410
GGGGACATTTTGTGGCTCTA
Chr2:20720300..20720319
59.93
50
downstream
ENSMUSE00000521501
Chr2:20723169..20723288
CTGTTAGCTCGGGACTGCTC
Chr2:20723239..20723258
60.16
60
downstream
ENSMUSE00000647331
Chr2:20727212..20727289
GGGCCATTTTCACATTCAAC
Chr2:20727273..20727292
60.18
45
downstream
ENSMUSE00000647330
Chr2:20727402..20729000
TCGGACTCCAGAGTCTTCGT
Chr2:20728283..20728302
59.99
55
downstream
ENSMUSE00000345647
Chr2:20729529..20729651
CCTGTAGTTTGGACTGCTTGC
Chr2:20729633..20729653
59.93
52.38
downstream
ENSMUSE00000699925
Chr2:20729529..20731981
CTGGCGAGGCTAGGAGTATG
Chr2:20730776..20730795
59.99
60
downstream
ENSMUSE00000699926
Chr2:20729529..20729817
CCTGTAGTTTGGACTGCTTGC
Chr2:20729633..20729653
59.93
52.38
downstream
ENSMUSE00000699956
Chr2:20729573..20729651
CCTGTAGTTTGGACTGCTTGC
Chr2:20729633..20729653
59.93
52.38
downstream
ENSMUSE00000391727
Chr2:20730337..20732151
GCTTGCGCTAGCGAATTATC
Chr2:20731513..20731532
60.11
50
downstream
ENSMUSE00000647329
Chr2:20730337..20731980
GCTTGCGCTAGCGAATTATC
Chr2:20731513..20731532
60.11
50
downstream
ENSMUSE00000699928
Chr2:20730337..20732340
GCTTGCGCTAGCGAATTATC
Chr2:20731513..20731532
60.11
50
downstream
ENSMUSE00000699942
Chr2:20730337..20732163
GCTTGCGCTAGCGAATTATC
Chr2:20731513..20731532
60.11
50
downstream
ENSMUSE00000699954
Chr2:20730337..20732151
GCTTGCGCTAGCGAATTATC
Chr2:20731513..20731532
60.11
50
downstream
ENSMUSE00000699974
Chr2:20730337..20732162
GCTTGCGCTAGCGAATTATC
Chr2:20731513..20731532
60.11
50
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
GTCCCACAGTCCTCAACCTC
Chr2:20583543..20583563
59.53
60
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
GTCCCACAGTCCTCAACCTC
Chr2:20583543..20583563
59.53
60
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000036617