Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI16014
Trapped Gene
B230112C05Rik (
ENSMUSG00000041817
)
Vector Insertion
Chr 13: 97884215 - 97888329
Public Clones
E039E07 (ggtc)
CMHD-GT_510F5-3 (cmhd)
Private Clones
OST467990 (lexicon)
Severity of mutation
(?)
Insertion after 55% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000297775 (Chr13:97884064..97884214 +)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
CTCCTGTTTCCACGCGTACT
Chr13:97884076..97884095
60.31
55
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000297775 (Chr13:97884064..97884214 +)
Downstram Exon
ENSMUSE00000297771 (Chr13:97888330..97888486 +)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
CTCCTGTTTCCACGCGTACT
Chr13:97884076..97884095
60.31
55
CTCTGATGTTCGTGCAGCAT
Chr13:97888360..97888379
60.02
50
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
upstream
ENSMUSE00000569672
Chr13:97876909..97877088
TGGCTTACGGTACCCACTGT
Chr13:97877051..97877070
60.43
55
upstream
ENSMUSE00000569671
Chr13:97879978..97880106
GTACCAGTCACCCGAGCATT
Chr13:97880061..97880080
60
55
upstream
ENSMUSE00000297785
Chr13:97881251..97881357
ACCTGGACTGGACGACACTC
Chr13:97881321..97881340
60.16
60
upstream
ENSMUSE00000297780
Chr13:97883594..97883633
TGCCTTTGCTAGCACTTCTG
Chr13:97883611..97883630
59.37
50
upstream
ENSMUSE00000297775
Chr13:97884064..97884214
CTCCTGTTTCCACGCGTACT
Chr13:97884076..97884095
60.31
55
*** Putative Vector Insertion (Chr 13: 97884215 - 97888329) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
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
TCTCACTCGCACTCTGTCGT
Chr13:97884232..97884252
59.76
55
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
TTGTTGCTTCTCGTGACTGG
Chr13:97884255..97884275
60.03
50
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000041817