Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI16376
Trapped Gene
Vps13b (
ENSMUSG00000037646
)
Vector Insertion
Chr 15: 35378477 - 35381852
Public Clones
IST13042F2 (tigm)
IST13042E2 (tigm)
Private Clones
OST462018 (lexicon)
Severity of mutation
(?)
Insertion after 0% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000624163 (Chr15:35378285..35378476 +)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
TCTAGATTGCCGTCTGGACA
Chr15:35378376..35378395
59.39
50
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000624163 (Chr15:35378285..35378476 +)
Downstram Exon
ENSMUSE00000624162 (Chr15:35381853..35382022 +)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
TCTAGATTGCCGTCTGGACA
Chr15:35378376..35378395
59.39
50
CTCCCATGATGACAGGAAGC
Chr15:35382020..35382039
60.62
55
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000418943
Chr15:35301304..35301532
TCTGTGGCGTGTTTACCTTG
Chr15:35301324..35301343
59.76
50
upstream
ENSMUSE00000235032
Chr15:35301688..35301862
GGACGTGGTTCTCAGCAAAC
Chr15:35301814..35301833
60.7
55
upstream
ENSMUSE00000235026
Chr15:35308644..35308787
TGGCCATATCCATGAACTGA
Chr15:35308673..35308692
59.88
45
upstream
ENSMUSE00000235019
Chr15:35347266..35347386
CATCCATAAAACCCCGAAGA
Chr15:35347327..35347346
59.76
45
upstream
ENSMUSE00000624171
Chr15:35352063..35352230
GTGGGTGAGTTATGGGATCG
Chr15:35352191..35352210
60.19
55
upstream
ENSMUSE00000624170
Chr15:35352871..35353052
CAACTGATCTGGTGCTGAGG
Chr15:35352871..35352890
59.42
55
upstream
ENSMUSE00000624169
Chr15:35359865..35360039
TAATGCAGCTTGGGATTGCT
Chr15:35359932..35359951
60.74
45
upstream
ENSMUSE00000624168
Chr15:35368468..35368733
TTATTGCACAAAGGCGACTG
Chr15:35368703..35368722
59.87
45
upstream
ENSMUSE00000624167
Chr15:35375325..35375420
TTTGTGTTGGGAACAAGAAGG
Chr15:35375387..35375407
59.99
42.86
upstream
ENSMUSE00000624166
Chr15:35375793..35375915
TGTAGGTTGCAGAGCCATGT
Chr15:35375837..35375856
59.32
50
upstream
ENSMUSE00000624165
Chr15:35376378..35376515
TGGATGCAGCTCACCATAAG
Chr15:35376496..35376515
59.82
50
upstream
ENSMUSE00000624164
Chr15:35377440..35377527
ACAGAGGTTTGGTGCGTTTT
Chr15:35377466..35377485
59.64
45
upstream
ENSMUSE00000624163
Chr15:35378285..35378476
TCTAGATTGCCGTCTGGACA
Chr15:35378376..35378395
59.39
50
*** Putative Vector Insertion (Chr 15: 35378477 - 35381852) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000624162
Chr15:35381853..35382022
CTCCCATGATGACAGGAAGC
Chr15:35382020..35382039
60.62
55
downstream
ENSMUSE00000371182
Chr15:35384712..35384906
TGGCATTCGTGACGTTACTC
Chr15:35384739..35384758
59.72
50
downstream
ENSMUSE00000395644
Chr15:35386370..35386494
AGGGGATAATTGGTGCAGGT
Chr15:35386448..35386467
60.58
50
downstream
ENSMUSE00000483848
Chr15:35401638..35401819
TTGGGAGCTCAAAAATACCC
Chr15:35401690..35401709
59.02
45
downstream
ENSMUSE00000624161
Chr15:35463051..35463185
AGAGTTGGCAGGGGATTCTT
Chr15:35463084..35463103
60.07
50
downstream
ENSMUSE00000624160
Chr15:35463942..35464115
CCTGAAGCAAAGGGATCAAC
Chr15:35463983..35464002
59.67
50
downstream
ENSMUSE00000624159
Chr15:35501815..35501924
TTTGCTCGTTTCTGTGGTTG
Chr15:35501911..35501930
59.88
45
downstream
ENSMUSE00000624158
Chr15:35506134..35506281
GGCCTGATATGACTGCTGCT
Chr15:35506241..35506260
60.39
55
downstream
ENSMUSE00000356638
Chr15:35506194..35506281
GGCCTGATATGACTGCTGCT
Chr15:35506241..35506260
60.39
55
downstream
ENSMUSE00000234924
Chr15:35527150..35527277
TCTTCATGAACACGCAGCAC
Chr15:35527204..35527223
61.03
50
downstream
ENSMUSE00000624157
Chr15:35527150..35527277
TCTTCATGAACACGCAGCAC
Chr15:35527204..35527223
61.03
50
downstream
ENSMUSE00000125242
Chr15:35536885..35537119
GGCAGGTTGTCATTTGGAAT
Chr15:35536934..35536953
59.8
45
downstream
ENSMUSE00000125244
Chr15:35547353..35547573
CATAGGCTCCACAAGGGAAA
Chr15:35547447..35547466
60.07
50
downstream
ENSMUSE00000125243
Chr15:35553357..35553560
ACCTACGCTGCTCCAAACTG
Chr15:35553503..35553522
60.45
55
downstream
ENSMUSE00000125249
Chr15:35569608..35569779
CGAATCATCACCAGCTTGAA
Chr15:35569640..35569659
59.8
45
downstream
ENSMUSE00000125247
Chr15:35570285..35570399
CACATCCTGCACGTCTATGG
Chr15:35570346..35570365
60.14
55
downstream
ENSMUSE00000234905
Chr15:35572153..35572219
ATGTCCTGACTGCCAACCTT
Chr15:35572183..35572202
59.58
50
downstream
ENSMUSE00000234901
Chr15:35572601..35572651
No primer for this exon
downstream
ENSMUSE00000624156
Chr15:35572814..35572838
CCCCAACACTCTTCTCCAAG
Chr15:35572837..35572856
59.69
55
downstream
ENSMUSE00000624155
Chr15:35572841..35572867
TACAGGAAAGGAAGGCACCTC
Chr15:35572864..35572884
60.62
52.38
downstream
ENSMUSE00000624154
Chr15:35572871..35572918
CTAAGGGGTCGAACCAACAA
Chr15:35572908..35572927
59.96
50
downstream
ENSMUSE00000624153
Chr15:35572922..35572948
AGAAGAAAGGAAGGCAGGACA
Chr15:35572950..35572970
60.37
47.62
downstream
ENSMUSE00000624152
Chr15:35575728..35576136
GGTTAACTTGTGGCGGACAT
Chr15:35575829..35575848
59.86
50
downstream
ENSMUSE00000624151
Chr15:35582010..35582121
CGGATTATCAGCCTGAGGAG
Chr15:35582089..35582108
59.79
55
downstream
ENSMUSE00000624150
Chr15:35598456..35598659
CTGAGCAGTGCCGATATTGA
Chr15:35598558..35598577
59.97
50
downstream
ENSMUSE00000624149
Chr15:35601054..35601180
TGCTCCAGTTATTCGCACAG
Chr15:35601132..35601151
60.01
50
downstream
ENSMUSE00000624148
Chr15:35604564..35604707
GTTGATGGCTCCAATCCAGT
Chr15:35604697..35604716
59.93
50
downstream
ENSMUSE00000624147
Chr15:35638881..35639568
TTGTCTGGCAGATGACCTTG
Chr15:35639381..35639400
59.83
50
downstream
ENSMUSE00000624146
Chr15:35675402..35675539
CTGCAGCCACACGATGTTAT
Chr15:35675457..35675476
59.75
50
downstream
ENSMUSE00000624145
Chr15:35700211..35700618
TAGAGTCTGACGGGGTGGAG
Chr15:35700357..35700376
60.25
60
downstream
ENSMUSE00000624144
Chr15:35721794..35721996
GGAGGAATGATGATCCAAGG
Chr15:35721823..35721842
59.29
50
downstream
ENSMUSE00000624143
Chr15:35723589..35723793
CTGATTCGGGTACTGGCATT
Chr15:35723694..35723713
59.96
50
downstream
ENSMUSE00000624142
Chr15:35724060..35724244
CGTGATTCGTACAAGGGTGA
Chr15:35724181..35724200
59.57
50
downstream
ENSMUSE00000427778
Chr15:35763939..35764135
ACGCAACAAAAACCTTCTGG
Chr15:35763993..35764012
60.15
45
downstream
ENSMUSE00000234730
Chr15:35769630..35769811
AGATGAGCGAACTGGAAGGA
Chr15:35769773..35769792
59.95
50
downstream
ENSMUSE00000234721
Chr15:35771004..35771353
TTCACCACAGTTTGCATCGT
Chr15:35771208..35771227
60.16
45
downstream
ENSMUSE00000234713
Chr15:35776601..35776762
TGGAGACTCGCCAAAAGAAT
Chr15:35776725..35776744
59.81
45
downstream
ENSMUSE00000234707
Chr15:35799042..35799197
TGAGTGCTCGGACTTTGATG
Chr15:35799183..35799202
59.98
50
downstream
ENSMUSE00000234701
Chr15:35805317..35805580
CTTGACCAGTCCTCGTCTCC
Chr15:35805534..35805553
59.83
60
downstream
ENSMUSE00000234693
Chr15:35806135..35806218
TCGCTGCTGAACTTGAGAGT
Chr15:35806218..35806237
58.91
50
downstream
ENSMUSE00000234684
Chr15:35806397..35806572
TCAGGTTCGACATTTTGCAG
Chr15:35806545..35806564
59.84
45
downstream
ENSMUSE00000234676
Chr15:35807252..35807422
GATATGGGAACCGCACAATC
Chr15:35807293..35807312
60.16
50
downstream
ENSMUSE00000234672
Chr15:35808398..35808599
TTGGGCTATCCCACTGACTC
Chr15:35808432..35808451
60.07
55
downstream
ENSMUSE00000234666
Chr15:35809524..35809712
GGGAAAGCTCCGAGTCTGAT
Chr15:35809702..35809721
60.74
55
downstream
ENSMUSE00000234659
Chr15:35812644..35812790
ATGACTTGTATGCCGTGCTG
Chr15:35812696..35812715
59.75
50
downstream
ENSMUSE00000234653
Chr15:35814262..35814545
AGTTCCAAAGGGCACTGCTA
Chr15:35814522..35814541
59.88
50
downstream
ENSMUSE00000234646
Chr15:35816632..35816759
TACTGGGCATCTGTTGTGGA
Chr15:35816734..35816753
60.11
50
downstream
ENSMUSE00000234638
Chr15:35816938..35817137
CCACTCGGCTGTCATTTCTT
Chr15:35817104..35817123
60.26
50
downstream
ENSMUSE00000234631
Chr15:35835027..35835145
TTCCGGGGCTAGAATGATAA
Chr15:35835113..35835132
59.5
45
downstream
ENSMUSE00000234624
Chr15:35839902..35840704
CAAAGGTGAACTCGCTGACA
Chr15:35840338..35840357
60.03
50
downstream
ENSMUSE00000234619
Chr15:35844529..35844705
GTGCTTGACGAATGATGTGG
Chr15:35844698..35844717
60.12
50
downstream
ENSMUSE00000234615
Chr15:35846802..35846972
CGGTTGTAGTGCTCCTCGTC
Chr15:35846889..35846908
60.85
60
downstream
ENSMUSE00000234608
Chr15:35852942..35853118
TGGTGAATACCCCCATGATT
Chr15:35853076..35853095
59.87
45
downstream
ENSMUSE00000234602
Chr15:35855059..35855161
TATTTGACGTGGCTGTTTGG
Chr15:35855158..35855177
59.58
45
downstream
ENSMUSE00000234597
Chr15:35855796..35856045
TTCTGATGTCAGCAGCAAGC
Chr15:35855907..35855926
60.3
50
downstream
ENSMUSE00000624141
Chr15:35859610..35859849
GTGGGTCCACCAAATAATGG
Chr15:35859787..35859806
59.91
50
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
TGTTTGTGCTCTGGAACATGA
Chr15:35381428..35381449
60.29
42.86
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
TGTTTGTGCTCTGGAACATGA
Chr15:35381428..35381449
60.29
42.86
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000037646