Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3236
Trapped Gene
Pard3 (ENSMUSG00000025812)
Vector Insertion
Chr 8: 129830229 - 129830409
Public Clones AL0593 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 10% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000677935 (Chr8:129830230..129830408 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGGCCTTTCCACTTCTGTC Chr8:129830272..129830291 59.84 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000677935 (Chr8:129830230..129830408 +)
Downstram Exon
ENSMUSE00000314897 (Chr8:129830230..129830408 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGGCCTTTCCACTTCTGTC Chr8:129830272..129830291 59.84 55 CAGAAGTGGAAAGGCCAGTT Chr8:129830292..129830311 59.33 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000713048 Chr8:129588145..129588373 CATGAAAGTGACCGTGTGCT Chr8:129588253..129588272 59.75 50
upstream ENSMUSE00000716122 Chr8:129588145..129588373 CATGAAAGTGACCGTGTGCT Chr8:129588253..129588272 59.75 50
upstream ENSMUSE00000314916 Chr8:129685110..129685211 CATCCTCTGTGACGTTGCTG Chr8:129685178..129685197 60.46 55
upstream ENSMUSE00000677937 Chr8:129685110..129685211 CATCCTCTGTGACGTTGCTG Chr8:129685178..129685197 60.46 55
upstream ENSMUSE00000314907 Chr8:129800921..129801101 AATTGAGGTCACGCCTTCAG Chr8:129801070..129801089 60.26 50
upstream ENSMUSE00000677936 Chr8:129800921..129801101 AATTGAGGTCACGCCTTCAG Chr8:129801070..129801089 60.26 50
upstream ENSMUSE00000605613 Chr8:129830210..129830408 CTGGCCTTTCCACTTCTGTC Chr8:129830272..129830291 59.84 55

*** Putative Vector Insertion (Chr 8: 129830229 - 129830409) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000314897 Chr8:129830230..129830408 CAGAAGTGGAAAGGCCAGTT Chr8:129830292..129830311 59.33 50
downstream ENSMUSE00000677935 Chr8:129830230..129830408 CAGAAGTGGAAAGGCCAGTT Chr8:129830292..129830311 59.33 50
downstream ENSMUSE00000314887 Chr8:129847941..129848072 GTTGTCTCGCTGGAACTGGT Chr8:129848012..129848031 60.31 55
downstream ENSMUSE00000314877 Chr8:129881175..129881266 TTCTCCAATCCGGTATCAGC Chr8:129881248..129881267 60.04 50
downstream ENSMUSE00000153411 Chr8:129883627..129883710 TTGGGGACTTGTACGAGCTT Chr8:129883659..129883678 59.73 50
downstream ENSMUSE00000153413 Chr8:129894148..129894273 CTTTCTCCAACCGCTTCACT Chr8:129894185..129894204 59.47 50
downstream ENSMUSE00000153401 Chr8:129895396..129895778 TGAGGCGTGAGCACTATGAG Chr8:129895666..129895685 60.16 55
downstream ENSMUSE00000153409 Chr8:129900644..129900783 AGGTGATGCTGAATCCCAGT Chr8:129900676..129900695 59.53 50
downstream ENSMUSE00000153414 Chr8:129902086..129902214 ACGAAAGACCAGAAGGCTCA Chr8:129902187..129902206 59.99 50
downstream ENSMUSE00000153410 Chr8:129904365..129904403 AGTCTGCATCTGGCTTGGTT Chr8:129904394..129904413 59.87 50
downstream ENSMUSE00000153405 Chr8:129912410..129912598 TACCATCGGGTGTGAGAACA Chr8:129912452..129912471 59.96 50
downstream ENSMUSE00000314823 Chr8:129913228..129913398 GCTGGTCATTTACCCTCAGC Chr8:129913258..129913277 59.7 55
downstream ENSMUSE00000153408 Chr8:129922500..129922650 CGTTCTCGGTCATCCAGTTC Chr8:129922570..129922589 60.66 55
downstream ENSMUSE00000677932 Chr8:129924298..129925961 ACCGGGTGACAAAATATGGA Chr8:129924513..129924532 60.05 45
downstream ENSMUSE00000153402 Chr8:129929275..129929464 TGAATCCAACGTCATCATGG Chr8:129929412..129929431 60.33 45
downstream ENSMUSE00000153412 Chr8:129933456..129933604 CGAGAACCGGATCAACATCT Chr8:129933490..129933509 60.07 50
downstream ENSMUSE00000605612 Chr8:129933456..129933607 CGAGAACCGGATCAACATCT Chr8:129933490..129933509 60.07 50
downstream ENSMUSE00000153415 Chr8:129934629..129934673 TGCTCTCTGGTCATCCACTGT Chr8:129934674..129934694 60.88 52.38
downstream ENSMUSE00000153407 Chr8:129939470..129939697 GAAAGGAATGTTCCCGTTCA Chr8:129939582..129939601 59.91 45
downstream ENSMUSE00000153406 Chr8:129950422..129950653 ACCTCGAGCTTTCCTCTGTG Chr8:129950454..129950473 59.6 55
downstream ENSMUSE00000579236 Chr8:129956695..129956725 TCATCTCTTCTCCGGCTTCA Chr8:129956728..129956747 61.03 50
downstream ENSMUSE00000314792 Chr8:129984174..129984284 GCACCCTGTCCTCTTCTGAG Chr8:129984265..129984284 59.99 60
downstream ENSMUSE00000314786 Chr8:129998279..129998515 CAAACGTCCGATGGAAATCT Chr8:129998367..129998386 59.93 45
downstream ENSMUSE00000314783 Chr8:130116961..130117081 ACTCTTGCCGTAGACGCTGT Chr8:130117016..130117035 60.08 55
downstream ENSMUSE00000314779 Chr8:130126959..130127086 ACTTGAACCTCCACGGACAC Chr8:130127020..130127039 60.01 55
downstream ENSMUSE00000605614 Chr8:130134332..130134730 TCTGTTCAGCCTAGCCACCT Chr8:130134638..130134657 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AACGTGGTTGTTCATTTCTGC Chr8:129830181..129830202 60.03 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AACGTGGTTGTTCATTTCTGC Chr8:129830181..129830202 60.03 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025812