Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12567
Trapped Gene
Recql (ENSMUSG00000030243)
Vector Insertion
Chr 6: 142313176 - 142314035
Public Clones F060D03 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 76% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000650559 (Chr6:142314036..142314127 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GATGAAGTGTGGAACGCAGA Chr6:142314077..142314096 59.84 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000650559 (Chr6:142314036..142314127 -)
Downstram Exon
ENSMUSE00000650556 (Chr6:142312956..142313175 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GATGAAGTGTGGAACGCAGA Chr6:142314077..142314096 59.84 50 TTTCCCATCCAAGCATCAAT Chr6:142313036..142313055 60.27 40

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000689079 Chr6:142335542..142335607 No primer for this exon
upstream ENSMUSE00000689085 Chr6:142335542..142335556 No primer for this exon
upstream ENSMUSE00000720250 Chr6:142333049..142333096 CATTTGGATCTCCGGTTCAG Chr6:142333072..142333091 60.45 50
upstream ENSMUSE00000720639 Chr6:142333049..142333096 CATTTGGATCTCCGGTTCAG Chr6:142333072..142333091 60.45 50
upstream ENSMUSE00000296975 Chr6:142326673..142326870 CGACTTGGACACATCACCAG Chr6:142326691..142326710 60.15 55
upstream ENSMUSE00000689072 Chr6:142326673..142326870 CGACTTGGACACATCACCAG Chr6:142326691..142326710 60.15 55
upstream ENSMUSE00000196718 Chr6:142325301..142325480 CCATGGTTCGGAAAGGTAAA Chr6:142325456..142325475 59.79 45
upstream ENSMUSE00000689070 Chr6:142325301..142325480 CCATGGTTCGGAAAGGTAAA Chr6:142325456..142325475 59.79 45
upstream ENSMUSE00000196715 Chr6:142323340..142323446 TGTGATTTGCCCACTCATCT Chr6:142323417..142323436 59.09 45
upstream ENSMUSE00000689067 Chr6:142323340..142323446 TGTGATTTGCCCACTCATCT Chr6:142323417..142323436 59.09 45
upstream ENSMUSE00000196710 Chr6:142321336..142321534 GTGGATGAAGTGCATTGCTG Chr6:142321365..142321384 60.27 50
upstream ENSMUSE00000689064 Chr6:142321336..142321534 GTGGATGAAGTGCATTGCTG Chr6:142321365..142321384 60.27 50
upstream ENSMUSE00000196709 Chr6:142317811..142317977 CATCTTGAAGCGCCAGTTTC Chr6:142317942..142317961 60.91 50
upstream ENSMUSE00000689057 Chr6:142317811..142317977 CATCTTGAAGCGCCAGTTTC Chr6:142317942..142317961 60.91 50
upstream ENSMUSE00000196708 Chr6:142316993..142317074 AAGCCCTCAAGTGCTGAAGA Chr6:142317046..142317065 60.13 50
upstream ENSMUSE00000689055 Chr6:142316993..142317074 AAGCCCTCAAGTGCTGAAGA Chr6:142317046..142317065 60.13 50
upstream ENSMUSE00000196717 Chr6:142316001..142316149 ACACAGTGGTCAGCCAATGA Chr6:142316008..142316027 60.16 50
upstream ENSMUSE00000689054 Chr6:142316001..142316149 ACACAGTGGTCAGCCAATGA Chr6:142316008..142316027 60.16 50
upstream ENSMUSE00000196707 Chr6:142315794..142315911 GGGAATTGATAAGCCAGACG Chr6:142315863..142315882 59.53 50
upstream ENSMUSE00000689053 Chr6:142315794..142315911 GGGAATTGATAAGCCAGACG Chr6:142315863..142315882 59.53 50
upstream ENSMUSE00000196712 Chr6:142315187..142315325 GTATTACGGCTTTGGGGACA Chr6:142315275..142315294 59.82 50
upstream ENSMUSE00000440296 Chr6:142315187..142315325 GTATTACGGCTTTGGGGACA Chr6:142315275..142315294 59.82 50
upstream ENSMUSE00000650559 Chr6:142314036..142314127 GATGAAGTGTGGAACGCAGA Chr6:142314077..142314096 59.84 50

*** Putative Vector Insertion (Chr 6: 142313176 - 142314035) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000650556 Chr6:142312956..142313175 TTTCCCATCCAAGCATCAAT Chr6:142313036..142313055 60.27 40
downstream ENSMUSE00000650552 Chr6:142312067..142312196 CTAACGCTGCTCTGTGCTGA Chr6:142312046..142312065 60.49 55
downstream ENSMUSE00000513853 Chr6:142311326..142311389 CACCTGACGAGCTTCAGACA Chr6:142311341..142311360 60.18 55
downstream ENSMUSE00000650539 Chr6:142310420..142311389 CTTTCATCATACGGGGAGGA Chr6:142310438..142310457 59.89 50
downstream ENSMUSE00000689051 Chr6:142308436..142308512 CGGGGCAGAGGTAGTGTTTA Chr6:142308450..142308469 60.12 55
downstream ENSMUSE00000689078 Chr6:142306531..142306574 GGGATCTGATGCTCTTGTCTG Chr6:142306526..142306546 59.82 52.38
downstream ENSMUSE00000650548 Chr6:142298862..142299065 TGAGGTCAGCATGTTTTCCA Chr6:142298880..142298899 60.24 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATAATCGCCTTGCAGCACAT Chr6:142313965..142313985 60.64 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGGACGTGACTGGGAAAAC Chr6:142313969..142313989 59.56 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030243