Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14365
Trapped Gene
Slc44a2 (ENSMUSG00000057193)
Vector Insertion
Chr 9: 21146297 - 21146382
Public Clones FHCRC-GT-S16-6H1 (fhcrc)
Private Clones not available
Severity of mutation (?) Insertion after 8% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000638368 (Chr9:21146223..21146296 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGGCCATCGTAGGCTATGT Chr9:21146260..21146279 60.12 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000638368 (Chr9:21146223..21146296 +)
Downstram Exon
ENSMUSE00000638367 (Chr9:21146383..21146467 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGGCCATCGTAGGCTATGT Chr9:21146260..21146279 60.12 55 AGATCACCTTCCGAGGGTCT Chr9:21146418..21146437 60.07 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000584922 Chr9:21125265..21125295 GATCGGAAGGACGCAGTCTA Chr9:21125274..21125293 60.36 55
upstream ENSMUSE00000362854 Chr9:21142288..21142406 GGGAAGGATTCGCAGAATTA Chr9:21142373..21142392 59.12 45
upstream ENSMUSE00000638369 Chr9:21142885..21142933 GGACGCCTCAGAAATACGAC Chr9:21142885..21142904 59.7 55
upstream ENSMUSE00000638368 Chr9:21146223..21146296 CTGGCCATCGTAGGCTATGT Chr9:21146260..21146279 60.12 55

*** Putative Vector Insertion (Chr 9: 21146297 - 21146382) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000638367 Chr9:21146383..21146467 AGATCACCTTCCGAGGGTCT Chr9:21146418..21146437 60.07 55
downstream ENSMUSE00000638366 Chr9:21146627..21146711 TTGGCACACTTCACGATGTT Chr9:21146674..21146693 60.16 45
downstream ENSMUSE00000638365 Chr9:21146839..21146949 AAGGGTGAGATAGCGGTCTG Chr9:21146880..21146899 59.31 55
downstream ENSMUSE00000638364 Chr9:21147042..21147102 GGTGATAACCGCTGGACACT Chr9:21147092..21147111 60 55
downstream ENSMUSE00000638363 Chr9:21147187..21147310 CCATGTCCGTCCTCATAGGT Chr9:21147274..21147293 59.8 55
downstream ENSMUSE00000638361 Chr9:21147408..21147491 CCGGGCCTCTAGAATCTTGT Chr9:21147438..21147457 60.59 55
downstream ENSMUSE00000638359 Chr9:21147579..21147691 AGCAGGACGATGAACAGGAG Chr9:21147629..21147648 60.41 55
downstream ENSMUSE00000638358 Chr9:21149276..21149407 TAAAAGCCATCCAGGTCTGC Chr9:21149410..21149429 60.21 50
downstream ENSMUSE00000638356 Chr9:21149737..21149836 CGATGGCGATCAATATCCTT Chr9:21149817..21149836 59.88 45
downstream ENSMUSE00000638355 Chr9:21149923..21150015 AGGTCACCAGTGGGTAGAGC Chr9:21149972..21149991 59.18 60
downstream ENSMUSE00000638354 Chr9:21150353..21150437 GGTTGCAGGTTTTCCTCAGA Chr9:21150435..21150454 60.23 50
downstream ENSMUSE00000638353 Chr9:21151133..21151395 ATCATCAGGCTTCCGCATAG Chr9:21151354..21151373 60.2 50
downstream ENSMUSE00000638351 Chr9:21151479..21151573 TGATCTGCACGATGGCTAAG Chr9:21151537..21151556 59.97 50
downstream ENSMUSE00000638347 Chr9:21152327..21152430 TTGGCAAACTTGTTCTGTGC Chr9:21152351..21152370 59.89 45
downstream ENSMUSE00000638345 Chr9:21152519..21152592 GCATTCCTGGCTGAGGTACA Chr9:21152565..21152584 61.21 55
downstream ENSMUSE00000638344 Chr9:21152772..21152842 GAAGTTTGCCCAACAGGAAG Chr9:21152827..21152846 59.71 50
downstream ENSMUSE00000638343 Chr9:21152982..21153070 AATTCTGATCCGATGGGTGA Chr9:21153025..21153044 60.28 45
downstream ENSMUSE00000638342 Chr9:21156911..21156995 TGCCATAGACGCTGAAGAAG Chr9:21156968..21156987 59.17 50
downstream ENSMUSE00000638341 Chr9:21158126..21159469 ATGCCCCAGTCCTCTAGGTT Chr9:21158390..21158409 59.96 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCGTAGGCTATGTGGCTGTG Chr9:21146268..21146288 59.89 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCGTAGGCTATGTGGCTGTG Chr9:21146268..21146288 59.89 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000057193