Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9600
Trapped Gene
Phf3 (ENSMUSG00000048874)
Vector Insertion
Chr 1: 30868813 - 30869861
Public Clones RRB001 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 54% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000315429 (Chr1:30869862..30869997 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGAGAAGCCAGATGTGTCTGA Chr1:30869954..30869974 60.4 52.38 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000315429 (Chr1:30869862..30869997 -)
Downstram Exon
ENSMUSE00000349139 (Chr1:30868617..30868812 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGAGAAGCCAGATGTGTCTGA Chr1:30869954..30869974 60.4 52.38 TTGAAGACAACGCATCTGCT Chr1:30868674..30868693 59.6 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000630485 Chr1:30919832..30920101 GCAATGATCCCAATTTCCAG Chr1:30919848..30919867 60.27 45
upstream ENSMUSE00000630484 Chr1:30893950..30894111 TCACCTCGTTTAATGGCACA Chr1:30893952..30893971 60.11 45
upstream ENSMUSE00000315372 Chr1:30886705..30887316 CAGCCGAAGTTTTTCTCTGG Chr1:30886827..30886846 59.99 50
upstream ENSMUSE00000630482 Chr1:30886688..30886702 No primer for this exon
upstream ENSMUSE00000630483 Chr1:30886688..30888404 AACACTGGGCTATGGTGAGG Chr1:30887640..30887659 59.99 55
upstream ENSMUSE00000604101 Chr1:30881055..30881364 AGCCCACAGCGAAGATAAAA Chr1:30881159..30881178 59.85 45
upstream ENSMUSE00000630481 Chr1:30881055..30881364 AGCCCACAGCGAAGATAAAA Chr1:30881159..30881178 59.85 45
upstream ENSMUSE00000468070 Chr1:30877976..30878159 No primer for this exon
upstream ENSMUSE00000630480 Chr1:30877976..30878159 No primer for this exon
upstream ENSMUSE00000315471 Chr1:30877528..30877672 GCTACTTCCAAGCCTTCTGC Chr1:30877582..30877601 59.22 55
upstream ENSMUSE00000702069 Chr1:30877528..30877672 GCTACTTCCAAGCCTTCTGC Chr1:30877582..30877601 59.22 55
upstream ENSMUSE00000315459 Chr1:30876926..30877082 GCAAAGGTTGCCACAAAAAT Chr1:30877023..30877042 59.98 40
upstream ENSMUSE00000702068 Chr1:30876926..30877082 GCAAAGGTTGCCACAAAAAT Chr1:30877023..30877042 59.98 40
upstream ENSMUSE00000315449 Chr1:30873313..30873429 TGGAGACGAAGGGAGAACAG Chr1:30873317..30873336 60.38 55
upstream ENSMUSE00000702067 Chr1:30873313..30873429 TGGAGACGAAGGGAGAACAG Chr1:30873317..30873336 60.38 55
upstream ENSMUSE00000476485 Chr1:30870805..30870936 GGAAAGACGACCAATCACGA Chr1:30870882..30870901 61.05 50
upstream ENSMUSE00000551418 Chr1:30870416..30870936 CCATCGAGATCCAGGTAGGA Chr1:30870799..30870818 60.03 55
upstream ENSMUSE00000315429 Chr1:30869862..30869997 GGAGAAGCCAGATGTGTCTGA Chr1:30869954..30869974 60.4 52.38

*** Putative Vector Insertion (Chr 1: 30868813 - 30869861) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000349139 Chr1:30868617..30868812 TTGAAGACAACGCATCTGCT Chr1:30868674..30868693 59.6 45
downstream ENSMUSE00000398107 Chr1:30867528..30867675 GTTCAATCGAGCCAGAAAGG Chr1:30867599..30867618 59.81 50
downstream ENSMUSE00000315573 Chr1:30865568..30865657 TGCCACCTACTTGAATGCTG Chr1:30865605..30865624 59.86 50
downstream ENSMUSE00000315566 Chr1:30863014..30863209 ACACCATAGCGCTTTCTGCT Chr1:30863090..30863109 60.04 50
downstream ENSMUSE00000410830 Chr1:30859187..30862787 CCTCTCTTAGGCCGTGTCTG Chr1:30859804..30859823 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCATAGGTTGGGAGTCTTGC Chr1:30869846..30869866 59.7 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCATAGGTTGGGAGTCTTGC Chr1:30869846..30869866 59.7 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048874