Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20380
Trapped Gene
Gsk3b (ENSMUSG00000022812)
Vector Insertion
Chr 16: 38090700 - 38144345
Public Clones (sanger) (ggtc) D089H11 (ggtc) CMHD-GT_473E3-3 (cmhd) IST14906F9 (tigm)
IST10761F5 (tigm) IST11564F8 (tigm) IST13027A9 (tigm) IST11196D12 (tigm)
Private Clones OST365110 (lexicon) OST77947 (lexicon) OST53827 (lexicon) OST51048 (lexicon)
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000436954 (Chr16:38089610..38090699 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTTGCGGGAGAACTTAATGC Chr16:38090505..38090524 59.85 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000436954 (Chr16:38089610..38090699 +)
Downstram Exon
ENSMUSE00000436937 (Chr16:38144346..38144539 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTTGCGGGAGAACTTAATGC Chr16:38090505..38090524 59.85 50 TGGTTACCTTGCTGCCATCT Chr16:38144375..38144394 60.66 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000436954 Chr16:38089610..38090699 CTTGCGGGAGAACTTAATGC Chr16:38090505..38090524 59.85 50
upstream ENSMUSE00000700452 Chr16:38090374..38090699 CTTGCGGGAGAACTTAATGC Chr16:38090505..38090524 59.85 50

*** Putative Vector Insertion (Chr 16: 38090700 - 38144345) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000436937 Chr16:38144346..38144539 TGGTTACCTTGCTGCCATCT Chr16:38144375..38144394 60.66 50
downstream ENSMUSE00000130676 Chr16:38170750..38170833 No primer for this exon
downstream ENSMUSE00000130687 Chr16:38184521..38184631 AGTGTCTGCTTGGCTCGACT Chr16:38184615..38184634 60.21 55
downstream ENSMUSE00000130691 Chr16:38187897..38188027 ATGTCTCGATGGCAGATTCC Chr16:38187967..38187986 60.04 50
downstream ENSMUSE00000130685 Chr16:38191614..38191720 GGTGCCCTGTAGTACCGAGA Chr16:38191682..38191701 60.13 60
downstream ENSMUSE00000436470 Chr16:38193983..38194080 CCAACTGATCCACACCACTG Chr16:38194069..38194088 60 55
downstream ENSMUSE00000475152 Chr16:38208081..38208176 AATTTGCTCCCTTGTTGGTG Chr16:38208113..38208132 59.97 45
downstream ENSMUSE00000700451 Chr16:38217199..38217237 AATGTCCTGCTCCTGGTGAG Chr16:38217223..38217242 60.26 55
downstream ENSMUSE00000436458 Chr16:38220058..38220244 CGCAATTCATCGAAAAATGA Chr16:38220182..38220201 59.64 35
downstream ENSMUSE00000436452 Chr16:38228764..38228862 GAGCATGTGGAGGGATAAGG Chr16:38228817..38228836 59.51 55
downstream ENSMUSE00000436942 Chr16:38240588..38241236 ATTGGTCTGTCCACGGTCTC Chr16:38240622..38240641 59.97 55
downstream ENSMUSE00000700450 Chr16:38240588..38240865 ATTGGTCTGTCCACGGTCTC Chr16:38240622..38240641 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATAATCGCCTTGCAGCACAT Chr16:38102750..38102770 60.64 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAAGTCGTGACTGGGAAAAC Chr16:38093746..38093766 58.19 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000022812