Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20252
Trapped Gene
Pard3 (ENSMUSG00000025812)
Vector Insertion
Chr 8: 129588374 - 129685109
Public Clones D093C12 (ggtc) D093C12 (ggtc) IST12426G10 (tigm) IST11176E4 (tigm)
IST10922D1 (tigm) IST15088C5 (tigm) IST11176E4 (tigm) IST10951D5 (tigm)
IST15079F6 (tigm) IST12823D4 (tigm)
Private Clones OST368752 (lexicon) OST347590 (lexicon) OST285118 (lexicon) OST148510 (lexicon)
OST135738 (lexicon) OST113332 (lexicon)
Severity of mutation (?) Insertion after 3% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000716122 (Chr8:129588145..129588373 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CATGAAAGTGACCGTGTGCT Chr8:129588253..129588272 59.75 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000716122 (Chr8:129588145..129588373 +)
Downstram Exon
ENSMUSE00000677937 (Chr8:129685110..129685211 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CATGAAAGTGACCGTGTGCT Chr8:129588253..129588272 59.75 50 TTGTCATCAGCAACGTCACA Chr8:129685207..129685226 59.87 45

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

*** Putative Vector Insertion (Chr 8: 129588374 - 129685109) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000314916 Chr8:129685110..129685211 TTGTCATCAGCAACGTCACA Chr8:129685207..129685226 59.87 45
downstream ENSMUSE00000677937 Chr8:129685110..129685211 TTGTCATCAGCAACGTCACA Chr8:129685207..129685226 59.87 45
downstream ENSMUSE00000314907 Chr8:129800921..129801101 GAAGGCGTGACCTCAATTTC Chr8:129801090..129801109 59.68 50
downstream ENSMUSE00000677936 Chr8:129800921..129801101 GAAGGCGTGACCTCAATTTC Chr8:129801090..129801109 59.68 50
downstream ENSMUSE00000605613 Chr8:129830210..129830408 CAGAAGTGGAAAGGCCAGTT Chr8:129830292..129830311 59.33 50
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 TTGACCCTCTGTTCGGAGTC Chr8:129684343..129684363 60.24 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGACCCTCTGTTCGGAGTC Chr8:129684343..129684363 60.24 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025812