Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI10378
Trapped Gene
Fn1 (
ENSMUSG00000026193
)
Vector Insertion
Chr 1: 71637467 - 71639644
Public Clones
Ex180 (baygenomics)
Private Clones
not available
Severity of mutation
(?)
Insertion after 94% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000629675 (Chr1:71639645..71639809 -)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
TTGACCCTTACACGGTTTCC
Chr1:71639751..71639770
59.83
50
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000629675 (Chr1:71639645..71639809 -)
Downstram Exon
ENSMUSE00000629674 (Chr1:71637341..71637466 -)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
TTGACCCTTACACGGTTTCC
Chr1:71639751..71639770
59.83
50
CCCACTTCTCTCCGATCTTG
Chr1:71637397..71637416
59.8
55
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000544656
Chr1:71699406..71699746
CTCCTCCCATCCACTCAAGA
Chr1:71699556..71699575
60.19
55
upstream
ENSMUSE00000629712
Chr1:71698095..71698223
GGGTTTTAACTGCGAGAGCA
Chr1:71698104..71698123
60.39
50
upstream
ENSMUSE00000629711
Chr1:71697136..71697273
ATGAGCGCCCTAAAGATTCC
Chr1:71697197..71697216
60.55
50
upstream
ENSMUSE00000629710
Chr1:71695768..71695899
AAGATTGGCGACAAGTGGAG
Chr1:71695851..71695870
60.26
50
upstream
ENSMUSE00000629709
Chr1:71694583..71694720
CAATGGACGCATCACCTGTA
Chr1:71694592..71694611
60.54
50
upstream
ENSMUSE00000629708
Chr1:71692121..71692276
AAGGACAACCGAGGAAACCT
Chr1:71692198..71692217
59.97
50
upstream
ENSMUSE00000629707
Chr1:71689534..71689725
GAAGTCGCAAGGAAACAAGC
Chr1:71689582..71689601
60
50
upstream
ENSMUSE00000629706
Chr1:71688526..71688705
TCCTCCCGTTCACCTACAAC
Chr1:71688641..71688660
59.97
55
upstream
ENSMUSE00000629705
Chr1:71687726..71687902
AACCGGAATTACACCGACTG
Chr1:71687818..71687837
59.85
50
upstream
ENSMUSE00000629704
Chr1:71686866..71687018
GTATCGCATTGGGGATCAGT
Chr1:71686962..71686981
59.78
50
upstream
ENSMUSE00000629703
Chr1:71685031..71685159
ACGAGGAGGGACATATGCTG
Chr1:71685083..71685102
60.1
55
upstream
ENSMUSE00000629702
Chr1:71683826..71683969
GACCCGGACATTTTACCAGA
Chr1:71683931..71683950
59.79
50
upstream
ENSMUSE00000629701
Chr1:71678615..71678736
GAGCCTTCACACATCACCAA
Chr1:71678637..71678656
59.68
50
upstream
ENSMUSE00000629700
Chr1:71676240..71676417
CAGAGAAGTGACACGCTTCG
Chr1:71676273..71676292
59.77
55
upstream
ENSMUSE00000629699
Chr1:71675890..71676066
TGTGGCCACTTCTGAATCTG
Chr1:71676007..71676026
59.83
50
upstream
ENSMUSE00000629698
Chr1:71674982..71675110
TCCGTGAACATTCCTGACCT
Chr1:71675071..71675090
60.51
50
upstream
ENSMUSE00000629697
Chr1:71674631..71674720
TAGACCCCAGGCACCTATCA
Chr1:71674634..71674653
60.47
55
upstream
ENSMUSE00000629696
Chr1:71673737..71673931
AGAGCACACCCGTTTTCATC
Chr1:71673768..71673787
60.12
50
upstream
ENSMUSE00000629695
Chr1:71672548..71672820
CCGACGGACCTACAGTTTGT
Chr1:71672787..71672806
60.03
55
upstream
ENSMUSE00000629694
Chr1:71670652..71670918
TGGGTCTGAGTACACCGTGA
Chr1:71670712..71670731
60.15
55
upstream
ENSMUSE00000629693
Chr1:71667299..71667393
CAACACCGAGGTGACAGAGA
Chr1:71667346..71667365
59.86
55
upstream
ENSMUSE00000629692
Chr1:71665958..71666126
ATGCACCGATTGTCAACAGA
Chr1:71665968..71665987
60.12
45
upstream
ENSMUSE00000629691
Chr1:71665153..71665239
CTGTCTCCACCGACCAACTT
Chr1:71665218..71665237
60.15
55
upstream
ENSMUSE00000629690
Chr1:71661934..71662125
TGCCCCTATCTCTGATACCG
Chr1:71661943..71661962
60.05
55
upstream
ENSMUSE00000544622
Chr1:71660337..71660609
ACCCCGCTAAACTCTTCCAC
Chr1:71660525..71660544
60.5
55
upstream
ENSMUSE00000629689
Chr1:71659042..71659224
GACAATGCCGTGGTCCTAAC
Chr1:71659044..71659063
60.38
55
upstream
ENSMUSE00000629688
Chr1:71657503..71657592
CGAACAACATGAGAGCATCC
Chr1:71657527..71657546
59.24
50
upstream
ENSMUSE00000629687
Chr1:71655987..71656256
TATCACCGCCAACTCATTCA
Chr1:71656203..71656222
60.07
45
upstream
ENSMUSE00000629686
Chr1:71654478..71654594
CTGCTCATCAGTTGGGAACC
Chr1:71654525..71654544
60.66
55
upstream
ENSMUSE00000629685
Chr1:71653277..71653441
GCAAGCCAGTTTCCATCAAT
Chr1:71653287..71653306
60.08
45
upstream
ENSMUSE00000629684
Chr1:71652459..71652614
GACCACCACTCCCAAAAATG
Chr1:71652495..71652514
60.21
50
upstream
ENSMUSE00000544614
Chr1:71651544..71651657
GGTTCAAACTGCAGTGACCA
Chr1:71651544..71651563
59.73
50
upstream
ENSMUSE00000377635
Chr1:71650234..71650503
TGGATGTCGATTCCATCAAA
Chr1:71650448..71650467
59.86
40
upstream
ENSMUSE00000629683
Chr1:71648884..71649071
TGGATAGCACCCAGTGTTCA
Chr1:71648990..71649009
60.11
50
upstream
ENSMUSE00000629682
Chr1:71647775..71647862
CAAGGACACACTGACAAGCAG
Chr1:71647807..71647827
59.52
52.38
upstream
ENSMUSE00000629681
Chr1:71646864..71647040
GTGTGACGGACGCTACAGAG
Chr1:71646997..71647016
59.49
60
upstream
ENSMUSE00000629680
Chr1:71646177..71646266
GCCAGGCACTGACTACAAGA
Chr1:71646240..71646259
59.04
55
upstream
ENSMUSE00000629679
Chr1:71645789..71645968
GATCCCCTCCCAGAGAAGTG
Chr1:71645832..71645851
60.99
60
upstream
ENSMUSE00000629678
Chr1:71644948..71645037
CCAGGAACCGAGTACACCAT
Chr1:71645010..71645029
59.84
55
upstream
ENSMUSE00000629671
Chr1:71643855..71644246
CAAGACCATACCTGCCGAAT
Chr1:71644059..71644078
59.96
50
upstream
ENSMUSE00000629677
Chr1:71643855..71644321
GGGTATGACACCGAAAATGG
Chr1:71644198..71644217
60.05
50
upstream
ENSMUSE00000629676
Chr1:71642238..71642376
ACAAGGTTCGGGAAGAGGTT
Chr1:71642257..71642276
59.97
50
upstream
ENSMUSE00000629675
Chr1:71639645..71639809
TTGACCCTTACACGGTTTCC
Chr1:71639751..71639770
59.83
50
*** Putative Vector Insertion (Chr 1: 71637467 - 71639644) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000629674
Chr1:71637341..71637466
CCCACTTCTCTCCGATCTTG
Chr1:71637397..71637416
59.8
55
downstream
ENSMUSE00000629673
Chr1:71636672..71636778
TCGTCATAGCACGTTGCTTC
Chr1:71636735..71636754
60.02
50
downstream
ENSMUSE00000629672
Chr1:71633404..71633517
CAGGTCTACGGCAGTTGTCA
Chr1:71633465..71633484
59.9
55
downstream
ENSMUSE00000544580
Chr1:71632094..71632857
ATCTAGCGGCATGAAGCACT
Chr1:71632797..71632816
60.01
50
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
CACCCTCTCACTCCTCCATC
Chr1:71639604..71639624
59.64
60
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
CACCCTCTCACTCCTCCATC
Chr1:71639604..71639624
59.64
60
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000026193