Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31796
Trapped Gene
Ankrd35 (ENSMUSG00000038354)
Vector Insertion
Chr 3: 96484992 - 96485949
Public Clones IST13043B5 (tigm) IST10052D7 (tigm) IST10052B8 (tigm) IST14538D3 (tigm)
IST12656F6 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 19% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000334317 (Chr3:96484885..96484991 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCCCGAGTTAATGTCACAG Chr3:96484959..96484978 59.72 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000334317 (Chr3:96484885..96484991 +)
Downstram Exon
ENSMUSE00000369013 (Chr3:96485950..96486134 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCCCGAGTTAATGTCACAG Chr3:96484959..96484978 59.72 50 AAGAGCGTTGTGTCCCAAAC Chr3:96486061..96486080 60.16 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000410288 Chr3:96474054..96474372 TAGCCGAGTTGGGTTAGGAA Chr3:96474260..96474279 59.7 50
upstream ENSMUSE00000370295 Chr3:96482056..96482186 AGAAATGGAACCGACGTGAT Chr3:96482060..96482079 59.41 45
upstream ENSMUSE00000397790 Chr3:96483103..96483191 CTCCAAAGGCCTGACAGAGT Chr3:96483118..96483137 59.45 55
upstream ENSMUSE00000357628 Chr3:96483553..96483617 CTTCATTTGGCCACCATCTC Chr3:96483564..96483583 60.46 50
upstream ENSMUSE00000346384 Chr3:96484394..96484451 GCAGAAAATCGCAGTCCATT Chr3:96484421..96484440 60.22 45
upstream ENSMUSE00000384381 Chr3:96484550..96484620 TCCTGGACGTGCTGGATAAT Chr3:96484601..96484620 60.48 50
upstream ENSMUSE00000334317 Chr3:96484885..96484991 TGCCCGAGTTAATGTCACAG Chr3:96484959..96484978 59.72 50

*** Putative Vector Insertion (Chr 3: 96484992 - 96485949) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000369013 Chr3:96485950..96486134 AAGAGCGTTGTGTCCCAAAC Chr3:96486061..96486080 60.16 50
downstream ENSMUSE00000362130 Chr3:96486917..96486954 GAGATGGGTGATCTGGGTGT Chr3:96486955..96486974 59.77 55
downstream ENSMUSE00000354995 Chr3:96487106..96489097 CCGATGAGGTGGTTTGTCTT Chr3:96489075..96489094 59.97 50
downstream ENSMUSE00000248243 Chr3:96493069..96493158 GCTCGAGCTTCTTCAGCAAC Chr3:96493099..96493118 60.43 55
downstream ENSMUSE00000248237 Chr3:96493368..96493433 TTCGTGGTTCTTCTGGGAGT Chr3:96493391..96493410 59.7 50
downstream ENSMUSE00000438379 Chr3:96494115..96494957 TCAGGTCTGGAGTTCGTGTG Chr3:96494872..96494891 59.86 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGTGCCCGAGTTAATGTCAC Chr3:96484958..96484978 60.38 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTGCCCGAGTTAATGTCAC Chr3:96484958..96484978 60.38 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000038354