Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25474
Trapped Gene
Parva (ENSMUSG00000030770)
Vector Insertion
Chr 7: 119663343 - 119687690
Public Clones IST12712H1 (tigm)
Private Clones OST182593 (lexicon)
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000670737 (Chr7:119663215..119663342 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGATGATTGTGGCTGCAGTA Chr7:119663288..119663307 60.83 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000670737 (Chr7:119663215..119663342 +)
Downstram Exon
ENSMUSE00000303522 (Chr7:119687691..119687780 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGATGATTGTGGCTGCAGTA Chr7:119663288..119663307 60.83 50 GTTGATGGCGTTCATTCCTT Chr7:119687731..119687750 59.94 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000670743 Chr7:119571019..119571044 ATAGGAACCCATCCATGCAG Chr7:119571022..119571041 59.77 50
upstream ENSMUSE00000520285 Chr7:119571220..119571614 TGACTCGTTCTTGGGGAAAC Chr7:119571556..119571575 60.09 50
upstream ENSMUSE00000670742 Chr7:119571415..119571614 TGACTCGTTCTTGGGGAAAC Chr7:119571556..119571575 60.09 50
upstream ENSMUSE00000670737 Chr7:119663215..119663342 CGATGATTGTGGCTGCAGTA Chr7:119663288..119663307 60.83 50

*** Putative Vector Insertion (Chr 7: 119663343 - 119687690) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000303522 Chr7:119687691..119687780 GTTGATGGCGTTCATTCCTT Chr7:119687731..119687750 59.94 45
downstream ENSMUSE00000203073 Chr7:119688247..119688317 CATTGTCCGGACCTCATTCT Chr7:119688272..119688291 59.93 50
downstream ENSMUSE00000203068 Chr7:119691025..119691127 CGAGGTCCTTCACGATGATT Chr7:119691088..119691107 60.07 50
downstream ENSMUSE00000203061 Chr7:119703443..119703583 CTTCTGTTTCTGGGCGATCT Chr7:119703513..119703532 59.43 50
downstream ENSMUSE00000203055 Chr7:119711277..119711392 GTGCCCGGAAATATTGAGAC Chr7:119711348..119711367 59.39 50
downstream ENSMUSE00000203071 Chr7:119716385..119716443 CTGGAGGATCCCTTCTCGTT Chr7:119716408..119716427 60.59 55
downstream ENSMUSE00000670752 Chr7:119718869..119718888 No primer for this exon
downstream ENSMUSE00000203069 Chr7:119719914..119719975 ATGGTCAAACAGCGTGTCAA Chr7:119719948..119719967 60.16 45
downstream ENSMUSE00000203075 Chr7:119720450..119720518 No primer for this exon
downstream ENSMUSE00000203067 Chr7:119723170..119723271 GCTGTGCAGGGGTACAAAGT Chr7:119723241..119723260 60.18 55
downstream ENSMUSE00000203065 Chr7:119724464..119724536 ATGAGCTCAAAGGCAAAGGA Chr7:119724498..119724517 59.96 45
downstream ENSMUSE00000401341 Chr7:119732054..119732484 TCCTATGTTCAGGGGGACTG Chr7:119732449..119732468 59.92 55
downstream ENSMUSE00000471145 Chr7:119732054..119735202 CATGTGAAGTGAGGGGTCCT Chr7:119733822..119733841 59.96 55
downstream ENSMUSE00000670740 Chr7:119732054..119733143 TCCTATGTTCAGGGGGACTG Chr7:119732449..119732468 59.92 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCATTGCTTGGCTACCTTCC Chr7:119669337..119669357 60.21 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCATTGCTTGGCTACCTTCC Chr7:119669337..119669357 60.21 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030770