Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4185
Trapped Gene
Sall4 (ENSMUSG00000027547)
Vector Insertion
Chr 2: 168582301 - 168590593
Public Clones (sanger) (sanger) (sanger) AM0297 (sanger) (sanger) (sanger)
(sanger) (sanger) (sanger) E129C02 (ggtc) D045F03 (ggtc) D016G07 (ggtc)
(ggtc) P126F07 (ggtc) D143D04 (ggtc) D042A03 (ggtc) 3SD004B11 (ggtc)
(ggtc) P117F07 (ggtc) D062C01 (ggtc) D019A02 (ggtc) 3SD138B12 (ggtc)
(ggtc) D170D03 (ggtc) D042A06 (ggtc) 5SP137H07 (ggtc) (ggtc)
P126F07 (ggtc) D143D04 (ggtc) D025E05 (ggtc) 5SP102G07 (ggtc) (ggtc)
P117F07 (ggtc) D045F03 (ggtc) D018H02 (ggtc) (ggtc) P136F02 (ggtc)
D170D03 (ggtc) D042A06 (ggtc) 5SD004B11 (ggtc) (ggtc) P126A11 (ggtc)
D104C05 (ggtc) D025E05 (ggtc) 5SD138B12 (ggtc) (ggtc) (cmhd)
CMHD-GT_516F2-5S (cmhd) PST24119-NR (escells) PST22862-NR (escells) PST16261-NR (escells)
IST13192A2 (tigm) IST14560H3 (tigm) IST14378G3 (tigm) IST10945D7 (tigm)
IST14116D9 (tigm) IST10034C10 (tigm) IST10065A5 (tigm) IST10115D6 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 14% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000679259 (Chr2:168590594..168590618 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000679259 (Chr2:168590594..168590618 -)
Downstram Exon
ENSMUSE00000709955 (Chr2:168579934..168582300 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon GGGAGCTGTTTTCTCGACTG Chr2:168580116..168580135 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000708679 Chr2:168592412..168592701 AGCACATCAACTGGGAGGAG Chr2:168592482..168592501 60.26 55
upstream ENSMUSE00000711707 Chr2:168592412..168592701 AGCACATCAACTGGGAGGAG Chr2:168592482..168592501 60.26 55
upstream ENSMUSE00000719112 Chr2:168592412..168592701 AGCACATCAACTGGGAGGAG Chr2:168592482..168592501 60.26 55
upstream ENSMUSE00000679259 Chr2:168590594..168590618 No primer for this exon

*** Putative Vector Insertion (Chr 2: 168582301 - 168590593) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000661187 Chr2:168581266..168582300 GACACGGACACTTGCTGAGA Chr2:168581600..168581619 60.03 55
downstream ENSMUSE00000679262 Chr2:168581266..168582300 GACACGGACACTTGCTGAGA Chr2:168581600..168581619 60.03 55
downstream ENSMUSE00000679260 Chr2:168580415..168580629 GTGAACCCCAAGGTGTGTCT Chr2:168580528..168580547 59.86 55
downstream ENSMUSE00000708693 Chr2:168579934..168582300 GGGAGCTGTTTTCTCGACTG Chr2:168580116..168580135 59.99 55
downstream ENSMUSE00000709955 Chr2:168579934..168582300 GGGAGCTGTTTTCTCGACTG Chr2:168580116..168580135 59.99 55
downstream ENSMUSE00000232199 Chr2:168577954..168578240 GGCTGTGCTCGGATAAATGT Chr2:168578179..168578198 60.1 50
downstream ENSMUSE00000706061 Chr2:168577954..168578240 GGCTGTGCTCGGATAAATGT Chr2:168578179..168578198 60.1 50
downstream ENSMUSE00000706060 Chr2:168575306..168575960 TAGGATTGCCCAAGGCTATG Chr2:168575343..168575362 60.05 50
downstream ENSMUSE00000661186 Chr2:168573832..168575960 TACCCGCATTAGTCACCACA Chr2:168574996..168575015 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CACCCTTAGCTGGTGTGAGG Chr2:168584551..168584571 60.7 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CACCCTTAGCTGGTGTGAGG Chr2:168584551..168584571 60.7 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TCTCAGCAAGTGTCCGTGTC Chr2:168581620..168581640 60.03 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TGGGAGAGCTACACCGTGAC Chr2:168581562..168581582 61.28 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027547