Tools for the biologist enabling optimized use of gene trap clones
Homepage
|
Blast Search
|
GO Search
|
Advanced Search
|
About
UniTrap UNI5558
Trapped Gene
Srbd1 (
ENSMUSG00000024135
)
Vector Insertion
Chr 17: 86457108 - 86497851
Public Clones
YTA202 (baygenomics)
Private Clones
not available
Severity of mutation
(?)
Insertion after 41% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000605986 (Chr17:86497852..86497959 -)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
GGTGATCGGAAATGGAACTG
Chr17:86497928..86497947
60.32
50
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000605986 (Chr17:86497852..86497959 -)
Downstram Exon
ENSMUSE00000605985 (Chr17:86457016..86457107 -)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
GGTGATCGGAAATGGAACTG
Chr17:86497928..86497947
60.32
50
TCGGGGCTGACACTGTAGAT
Chr17:86457041..86457060
60.68
55
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000691064
Chr17:86544461..86544515
TCTTCTCCAGATTCGCCAAG
Chr17:86544468..86544487
60.47
50
upstream
ENSMUSE00000138626
Chr17:86541700..86541779
CATTGCGCAAAAGAGTGAAA
Chr17:86541753..86541772
59.99
40
upstream
ENSMUSE00000691063
Chr17:86541700..86541779
CATTGCGCAAAAGAGTGAAA
Chr17:86541753..86541772
59.99
40
upstream
ENSMUSE00000138628
Chr17:86538409..86538589
CGAAGAAGAGCTCCCAACAG
Chr17:86538451..86538470
60.13
55
upstream
ENSMUSE00000138631
Chr17:86535786..86535875
CCACAAGTTGCAGACGACAA
Chr17:86535812..86535831
60.91
50
upstream
ENSMUSE00000605996
Chr17:86535504..86535875
GAGAGCGAGGACAGCTTCAC
Chr17:86535628..86535647
60.29
60
upstream
ENSMUSE00000605995
Chr17:86529454..86529620
GCCAACATCATACGCCTCTT
Chr17:86529562..86529581
60.1
50
upstream
ENSMUSE00000605994
Chr17:86527056..86527173
AAAATGTCGGAGTGCTTGCT
Chr17:86527102..86527121
59.88
45
upstream
ENSMUSE00000605993
Chr17:86525451..86525589
CTAGAAGGAGCAGCGTGGAC
Chr17:86525510..86525529
60.16
60
upstream
ENSMUSE00000605992
Chr17:86519990..86520086
GCCTTTCTGAGCTCAACGAT
Chr17:86520067..86520086
59.58
50
upstream
ENSMUSE00000691065
Chr17:86519990..86520062
No primer for this exon
upstream
ENSMUSE00000605991
Chr17:86519254..86519389
TGCAACATAAGGACCATCCA
Chr17:86519264..86519283
59.92
45
upstream
ENSMUSE00000605990
Chr17:86514533..86514636
GCCATTAACCGAGGAGAGAA
Chr17:86514611..86514630
59.27
50
upstream
ENSMUSE00000605989
Chr17:86508567..86508674
TCCTTTAAGCGCCTCATTGT
Chr17:86508591..86508610
59.85
45
upstream
ENSMUSE00000605988
Chr17:86502183..86502340
TGGATGCAAACTAGCCATCA
Chr17:86502195..86502214
60.22
45
upstream
ENSMUSE00000605987
Chr17:86498545..86498635
TCAGATCCTTCACACGGATG
Chr17:86498615..86498634
59.63
50
upstream
ENSMUSE00000605986
Chr17:86497852..86497959
GGTGATCGGAAATGGAACTG
Chr17:86497928..86497947
60.32
50
*** Putative Vector Insertion (Chr 17: 86457108 - 86497851) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000605985
Chr17:86457016..86457107
TCGGGGCTGACACTGTAGAT
Chr17:86457041..86457060
60.68
55
downstream
ENSMUSE00000605984
Chr17:86450426..86450508
GATCTTGAACACGCCTTGCT
Chr17:86450460..86450479
60.41
50
downstream
ENSMUSE00000656923
Chr17:86450407..86450508
GATCTTGAACACGCCTTGCT
Chr17:86450460..86450479
60.41
50
downstream
ENSMUSE00000656922
Chr17:86444217..86444296
TCCTGTAAACCCCTCCCTCT
Chr17:86444242..86444261
59.93
55
downstream
ENSMUSE00000605983
Chr17:86403187..86403293
ATCCACTCCCACAAAGCTGA
Chr17:86403194..86403213
60.66
50
downstream
ENSMUSE00000361942
Chr17:86400771..86400947
TGCAGAATGTCCGGATGTAA
Chr17:86400750..86400769
60.07
45
downstream
ENSMUSE00000539262
Chr17:86399661..86399816
AGTCTGGTCCAGTGGGTTTG
Chr17:86399674..86399693
60
55
downstream
ENSMUSE00000605980
Chr17:86399661..86399813
AGTCTGGTCCAGTGGGTTTG
Chr17:86399674..86399693
60
55
downstream
ENSMUSE00000375453
Chr17:86387665..86387849
TCTTTCCCGAGAGACACGTT
Chr17:86387744..86387763
59.84
50
downstream
ENSMUSE00000605979
Chr17:86384006..86384823
TGAACCGGATAGGAATCAGC
Chr17:86384649..86384668
60.04
50
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
GTCATTTAATCGCCTTGCAG
Chr17:86476786..86476806
58.39
45
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
ATGGCCTGCTTTACGTGACT
Chr17:86476793..86476813
59.76
50
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000024135