Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI17846
Trapped Gene
Frmd5 (ENSMUSG00000027238)
Vector Insertion
Chr 2: 121417499 - 121590766
Public Clones (sanger) (sanger) E048E06 (ggtc) E048E06 (ggtc) IST11592F9 (tigm)
IST14623E9 (tigm) IST12866H1 (tigm) IST10246C5 (tigm) IST14765H5 (tigm)
Private Clones OST435036 (lexicon) OST431367 (lexicon) OST431213 (lexicon) OST402557 (lexicon)
OST390703 (lexicon) OST319383 (lexicon) OST309055 (lexicon) OST300888 (lexicon)
OST296477 (lexicon) OST257846 (lexicon) OST234501 (lexicon) OST181806 (lexicon)
OST174438 (lexicon) OST116445 (lexicon) OST66995 (lexicon) OST60828 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000684543 (Chr2:121590767..121590820 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCCTGAAGGAAAGCCATAGA Chr2:121590779..121590798 59.41 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000684543 (Chr2:121590767..121590820 -)
Downstram Exon
ENSMUSE00000684541 (Chr2:121417394..121417498 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCCTGAAGGAAAGCCATAGA Chr2:121590779..121590798 59.41 50 CCACAAAACGAATCCCAAAG Chr2:121417389..121417408 60.34 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000480909 Chr2:121632466..121632567 AGCGAGTACACCTGCACCAT Chr2:121632470..121632489 60.74 55
upstream ENSMUSE00000684499 Chr2:121632466..121632728 AGCGAGTACACCTGCACCAT Chr2:121632470..121632489 60.74 55
upstream ENSMUSE00000721070 Chr2:121612998..121613080 CCAGAGACAGCTTCCTCGTC Chr2:121613002..121613021 60.13 60
upstream ENSMUSE00000684543 Chr2:121590767..121590820 GCCTGAAGGAAAGCCATAGA Chr2:121590779..121590798 59.41 50

*** Putative Vector Insertion (Chr 2: 121417499 - 121590766) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000427046 Chr2:121417394..121417498 CCACAAAACGAATCCCAAAG Chr2:121417389..121417408 60.34 45
downstream ENSMUSE00000684541 Chr2:121417394..121417498 CCACAAAACGAATCCCAAAG Chr2:121417389..121417408 60.34 45
downstream ENSMUSE00000426073 Chr2:121412165..121412207 CAGCTGCTTCACCACTGACT Chr2:121412147..121412166 59.21 55
downstream ENSMUSE00000684539 Chr2:121412165..121412207 CAGCTGCTTCACCACTGACT Chr2:121412147..121412166 59.21 55
downstream ENSMUSE00000427062 Chr2:121411642..121411720 GGTCGGCAGGGTAAAACTTC Chr2:121411648..121411667 60.86 55
downstream ENSMUSE00000684538 Chr2:121411642..121411720 GGTCGGCAGGGTAAAACTTC Chr2:121411648..121411667 60.86 55
downstream ENSMUSE00000715077 Chr2:121411642..121411720 GGTCGGCAGGGTAAAACTTC Chr2:121411648..121411667 60.86 55
downstream ENSMUSE00000292220 Chr2:121402058..121402155 GCCGTGGTAGAGATCCCTTT Chr2:121402091..121402110 60.46 55
downstream ENSMUSE00000292212 Chr2:121399281..121399404 TGTTTCGGGAAAAATTGGAA Chr2:121399310..121399329 60.27 35
downstream ENSMUSE00000292204 Chr2:121394629..121394716 AGGGTCCACTCCGTAGGTCT Chr2:121394619..121394638 59.99 60
downstream ENSMUSE00000351539 Chr2:121388621..121388709 GAACAACAAACCCGAAAGGA Chr2:121388633..121388652 59.95 45
downstream ENSMUSE00000392408 Chr2:121383560..121383623 TCAGCTTGGTCACCTCATTC Chr2:121383582..121383601 58.8 50
downstream ENSMUSE00000344482 Chr2:121383053..121383144 AGGCTTGGTTCTCAATTCCA Chr2:121383038..121383057 59.67 45
downstream ENSMUSE00000401873 Chr2:121381306..121381380 GAACAAATTGCTGCTGGACA Chr2:121381310..121381329 59.85 45
downstream ENSMUSE00000360386 Chr2:121380001..121380069 TTGATCTTGGCACTGGACTC Chr2:121380003..121380022 58.8 50
downstream ENSMUSE00000395442 Chr2:121379074..121379180 TGTGCACAGCTCTTCTTCGT Chr2:121379067..121379086 59.78 50
downstream ENSMUSE00000487836 Chr2:121374625..121374968 TGTAGGCCTCATCCGCTATC Chr2:121374809..121374828 60.2 55
downstream ENSMUSE00000684493 Chr2:121374398..121374445 CTCACCACTGAGCGGATTTT Chr2:121374388..121374407 60.26 50
downstream ENSMUSE00000684497 Chr2:121374391..121374968 AGGAGTCCCATGGTCACAAG Chr2:121374547..121374566 59.96 55
downstream ENSMUSE00000684498 Chr2:121374043..121374968 AGGAGTCCCATGGTCACAAG Chr2:121374547..121374566 59.96 55
downstream ENSMUSE00000721682 Chr2:121373823..121374968 AGGAGTCCCATGGTCACAAG Chr2:121374547..121374566 59.96 55
downstream ENSMUSE00000597501 Chr2:121373708..121373759 CTGTAGCTGTGGTCCCTTCAG Chr2:121373708..121373728 59.92 57.14
downstream ENSMUSE00000684507 Chr2:121373617..121373633 No primer for this exon
downstream ENSMUSE00000684501 Chr2:121371267..121373759 GATTTGGCACACGAAAGGTT Chr2:121371363..121371382 59.98 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATTAATCGCCTTGCAGCAC Chr2:121578698..121578718 58.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCATTGAGGGAGAGGGAGAG Chr2:121422715..121422735 61.12 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TGATGACTGTGTGCGAGGAG Chr2:121578775..121578795 61.06 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GCCATTCCTTTGCCTTGTTA Chr2:121422771..121422791 60.07 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027238