Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI9104
Trapped Gene
B230112C05Rik (
ENSMUSG00000041817
)
Vector Insertion
Chr 13: 97867667 - 97876908
Public Clones
(sanger)
XK517 (baygenomics)
D063C11 (ggtc)
D063C11 (ggtc)
Private Clones
OST360783 (lexicon)
OST311408 (lexicon)
OST308181 (lexicon)
OST41872 (lexicon)
Severity of mutation
(?)
Insertion after 25% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000297802 (Chr13:97867495..97867666 +)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
GAGGCCGTTGGGTTTTATTC
Chr13:97867633..97867652
60.67
50
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000297802 (Chr13:97867495..97867666 +)
Downstram Exon
ENSMUSE00000569672 (Chr13:97876909..97877088 +)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
GAGGCCGTTGGGTTTTATTC
Chr13:97867633..97867652
60.67
50
AGCCCCAAATCTTTTCCTCT
Chr13:97877008..97877027
59.17
45
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000611533
Chr13:97841598..97841666
No primer for this exon
upstream
ENSMUSE00000297815
Chr13:97861773..97861907
GATAACTGCACGCATGAGGA
Chr13:97861800..97861819
59.83
50
upstream
ENSMUSE00000297810
Chr13:97863546..97863645
TTTGCGCCTGAAGATTCTCT
Chr13:97863621..97863640
60.1
45
upstream
ENSMUSE00000297805
Chr13:97864017..97864102
GGTGGGCCATTGATGATATT
Chr13:97864044..97864063
59.47
45
upstream
ENSMUSE00000297802
Chr13:97867495..97867666
GAGGCCGTTGGGTTTTATTC
Chr13:97867633..97867652
60.67
50
*** Putative Vector Insertion (Chr 13: 97867667 - 97876908) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000569672
Chr13:97876909..97877088
AGCCCCAAATCTTTTCCTCT
Chr13:97877008..97877027
59.17
45
downstream
ENSMUSE00000569671
Chr13:97879978..97880106
TGACTGGTACTCGCTGATGC
Chr13:97880073..97880092
60.02
55
downstream
ENSMUSE00000297785
Chr13:97881251..97881357
GAGTGTCGTCCAGTCCAGGT
Chr13:97881343..97881362
60.16
60
downstream
ENSMUSE00000297780
Chr13:97883594..97883633
GGCATCTTTTAGGGAATGGA
Chr13:97883617..97883636
58.97
45
downstream
ENSMUSE00000297775
Chr13:97884064..97884214
GTACGCGTGGAAACAGGAGT
Chr13:97884097..97884116
60.18
55
downstream
ENSMUSE00000297771
Chr13:97888330..97888486
CTCTGATGTTCGTGCAGCAT
Chr13:97888360..97888379
60.02
50
downstream
ENSMUSE00000297764
Chr13:97892647..97892847
CTGGTGGAGTCCTCGTCTTC
Chr13:97892735..97892754
59.83
60
downstream
ENSMUSE00000397821
Chr13:97896451..97899470
GGCGCGTCTTCAAGTTCTAC
Chr13:97896782..97896801
60.02
55
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
AACTAATCGCCTTGCAGCAC
Chr13:97873715..97873735
60.42
50
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
GAGGCCGTTGGGTTTTATTC
Chr13:97873634..97873654
60.67
50
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000041817