Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI23070
Trapped Gene
Ccdc38 (
ENSMUSG00000036168
)
Vector Insertion
Chr 10: 93008251 - 93011653
Public Clones
IST10357E5 (tigm)
Private Clones
OST277435 (lexicon)
OST167706 (lexicon)
Severity of mutation
(?)
Insertion after 2% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000343884 (Chr10:93008200..93008250 +)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
TCCCAGATGCACACATCAAT
Chr10:93008220..93008239
59.92
45
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000343884 (Chr10:93008200..93008250 +)
Downstram Exon
ENSMUSE00000376652 (Chr10:93011654..93011754 +)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
TCCCAGATGCACACATCAAT
Chr10:93008220..93008239
59.92
45
TTCCTGGCAGCAATTTCATT
Chr10:93011753..93011772
60.58
40
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000665682
Chr10:93003377..93003554
CAGTTTGGTGCCTCTGTCTG
Chr10:93003477..93003496
59.46
55
upstream
ENSMUSE00000343884
Chr10:93008200..93008250
TCCCAGATGCACACATCAAT
Chr10:93008220..93008239
59.92
45
*** Putative Vector Insertion (Chr 10: 93008251 - 93011653) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000376652
Chr10:93011654..93011754
TTCCTGGCAGCAATTTCATT
Chr10:93011753..93011772
60.58
40
downstream
ENSMUSE00000261666
Chr10:93012907..93013072
CCCAGACGTTCATAGGAGGA
Chr10:93013040..93013059
60.06
55
downstream
ENSMUSE00000574124
Chr10:93018264..93018328
AACTCGTGGACCGTCCTCTT
Chr10:93018297..93018316
61.08
55
downstream
ENSMUSE00000640905
Chr10:93025476..93025639
AATGCGTCATCTTGGAGCTT
Chr10:93025585..93025604
59.84
45
downstream
ENSMUSE00000640904
Chr10:93025950..93026030
CCATGCTTGCTTTCTTGAGC
Chr10:93026014..93026033
61.05
50
downstream
ENSMUSE00000640903
Chr10:93028539..93028690
GTGGTTGCTTTTGGACGACT
Chr10:93028671..93028690
60.16
50
downstream
ENSMUSE00000640902
Chr10:93030409..93030501
CTCGCCTTGAACTCCATTCT
Chr10:93030495..93030514
59.43
50
downstream
ENSMUSE00000640901
Chr10:93032621..93032678
TTGGCCCAAAGTATGTTTCC
Chr10:93032655..93032674
59.8
45
downstream
ENSMUSE00000640900
Chr10:93033592..93033664
No primer for this exon
downstream
ENSMUSE00000640899
Chr10:93036756..93036907
GAACCAAGGTGAGGTTCTGC
Chr10:93036840..93036859
59.7
55
downstream
ENSMUSE00000640898
Chr10:93038018..93038153
CCTTCTCCTCCTCTCGTTCA
Chr10:93038094..93038113
59.53
55
downstream
ENSMUSE00000574123
Chr10:93041454..93041636
GCTTTCCATGTAGGCTCCTG
Chr10:93041494..93041513
59.84
55
downstream
ENSMUSE00000640897
Chr10:93042507..93042712
ATCGCTTCCACGTGTTCTCT
Chr10:93042682..93042701
59.87
50
downstream
ENSMUSE00000640896
Chr10:93044478..93044571
TTCCAGAGCAGCTTTTAGCC
Chr10:93044547..93044566
59.73
50
downstream
ENSMUSE00000574122
Chr10:93045187..93047071
GTACATAGATGGGGCGCTGT
Chr10:93046825..93046844
59.99
55
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
TCCCAGATGCACACATCAAT
Chr10:93011221..93011241
59.92
45
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
TCCCAGATGCACACATCAAT
Chr10:93011221..93011241
59.92
45
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000036168