Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13304
Trapped Gene
Abl1 (ENSMUSG00000026842)
Vector Insertion
Chr 2: 31615976 - 31633853
Public Clones CMHD-GT_329A6-3 (cmhd) IST14374F7 (tigm) IST14234G2 (tigm) IST14387B1 (tigm)
IST10055A5 (tigm) IST12712D9 (tigm) IST10070E5 (tigm) IST10845G1 (tigm)
IST10898D9 (tigm) IST14387C1 (tigm) IST13375A12 (tigm)
Private Clones OST284481 (lexicon) OST220388 (lexicon) OST169194 (lexicon) OST130711 (lexicon)
OST52877 (lexicon)
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000695641 (Chr2:31615912..31615975 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTGGACCTACACCAAGTGC Chr2:31615922..31615941 60.43 60 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000695641 (Chr2:31615912..31615975 +)
Downstram Exon
ENSMUSE00000604210 (Chr2:31633854..31634027 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTGGACCTACACCAAGTGC Chr2:31615922..31615941 60.43 60 GAGTTCCATCGAGCTGCTTC Chr2:31633926..31633945 60.1 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000478509 Chr2:31544833..31545462 ACTTTTGGCATTGCGGTTAC Chr2:31545076..31545095 60 45
upstream ENSMUSE00000695649 Chr2:31546219..31546279 AGCTGCACTTGAAACTTCTCG Chr2:31546247..31546267 59.81 47.62
upstream ENSMUSE00000352617 Chr2:31615500..31615635 CTTCGTCCTCCAGCTGCTAC Chr2:31615609..31615628 60.16 60
upstream ENSMUSE00000695641 Chr2:31615912..31615975 GGTGGACCTACACCAAGTGC Chr2:31615922..31615941 60.43 60

*** Putative Vector Insertion (Chr 2: 31615976 - 31633853) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000604210 Chr2:31633854..31634027 GAGTTCCATCGAGCTGCTTC Chr2:31633926..31633945 60.1 55
downstream ENSMUSE00000604209 Chr2:31634441..31634736 CAGCAGCATTCCGAGATACA Chr2:31634602..31634621 59.97 50
downstream ENSMUSE00000604208 Chr2:31640027..31640299 GCTGGGTAGTGGAGTGTGGT Chr2:31640130..31640149 60.03 60
downstream ENSMUSE00000604207 Chr2:31645791..31645875 CTGCACCAGGTTAGGGTGTT Chr2:31645871..31645890 60.03 55
downstream ENSMUSE00000604206 Chr2:31646182..31646359 CAGGTAGTCCAGCAGGTTCC Chr2:31646258..31646277 59.72 60
downstream ENSMUSE00000604205 Chr2:31647758..31647942 GTTGTAGGCCAGGCTCTCAG Chr2:31647917..31647936 60.01 60
downstream ENSMUSE00000604204 Chr2:31650062..31650214 GGTAGCAATCTCCCAGAGCA Chr2:31650096..31650115 60.36 55
downstream ENSMUSE00000604203 Chr2:31652493..31652582 TCAAAGGCTTGGTGGATTTC Chr2:31652553..31652572 60.05 45
downstream ENSMUSE00000604202 Chr2:31653083..31653247 CTCTCCTGCAGGTTCTGGTC Chr2:31653184..31653203 59.99 60
downstream ENSMUSE00000346836 Chr2:31655726..31659747 GGACTTGGTAGGCTCTGCTG Chr2:31656024..31656043 60.01 60
downstream ENSMUSE00000604211 Chr2:31655726..31659054 GGACTTGGTAGGCTCTGCTG Chr2:31656024..31656043 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGATCCCGCTCTACCATTTA Chr2:31615954..31615974 59 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTTTCTGCAGACGTGACTGG Chr2:31616016..31616036 59.62 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026842