Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2660
Trapped Gene
Taf1a (ENSMUSG00000072258)
Vector Insertion
Chr NT_165754: 376099 - 377674
Public Clones AL0579 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 54% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000679196 (ChrNT_165754:375968..376098 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCTGTGCACTGGTCAAAACC ChrNT_165754:376040..376059 59.73 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000679196 (ChrNT_165754:375968..376098 +)
Downstram Exon
ENSMUSE00000679195 (ChrNT_165754:377675..377833 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCTGTGCACTGGTCAAAACC ChrNT_165754:376040..376059 59.73 50 CGACGGGAACTTCTCATCAT ChrNT_165754:377755..377774 60.07 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000679200 ChrNT_165754:362233..362438 AAGCGCTCGTTAACTGCTTC ChrNT_165754:362308..362327 59.8 50
upstream ENSMUSE00000628382 ChrNT_165754:364269..364392 CAGAAACGTCGGTGCTCTCT ChrNT_165754:364324..364343 60.59 55
upstream ENSMUSE00000628381 ChrNT_165754:369258..369427 TTTGCTCAGACGACAAGTGC ChrNT_165754:369284..369303 60.18 50
upstream ENSMUSE00000628380 ChrNT_165754:371128..371241 TACCACCCCAAAAGCAATGT ChrNT_165754:371161..371180 60.23 45
upstream ENSMUSE00000679197 ChrNT_165754:373951..374149 AATGCTTGATGATGCGAACA ChrNT_165754:373989..374008 60.23 40
upstream ENSMUSE00000679196 ChrNT_165754:375968..376098 TCTGTGCACTGGTCAAAACC ChrNT_165754:376040..376059 59.73 50

*** Putative Vector Insertion (Chr NT_165754: 376099 - 377674) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000679195 ChrNT_165754:377675..377833 CGACGGGAACTTCTCATCAT ChrNT_165754:377755..377774 60.07 50
downstream ENSMUSE00000679194 ChrNT_165754:379244..379310 GGGATGGCACAATCTCATGT ChrNT_165754:379271..379290 60.76 50
downstream ENSMUSE00000679193 ChrNT_165754:379892..379983 TTTCCAGGCCGTTATGTTCT ChrNT_165754:379983..380002 59.57 45
downstream ENSMUSE00000679192 ChrNT_165754:381764..381780 No primer for this exon
downstream ENSMUSE00000679191 ChrNT_165754:381915..381929 No primer for this exon
downstream ENSMUSE00000679190 ChrNT_165754:381957..382111 CACTCTTCGCCCAAAAGAAG ChrNT_165754:382048..382067 59.99 50
downstream ENSMUSE00000679189 ChrNT_165754:382583..382701 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGGGATCCTTTTGTGAAGAG ChrNT_165754:376069..376090 58.78 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGGGATCCTTTTGTGAAGAG ChrNT_165754:376069..376090 58.78 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000072258