Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI36417
Trapped Gene
Atg2a (ENSMUSG00000024773)
Vector Insertion
Chr 19: 6251864 - 6252426
Public Clones IST13146F11 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 48% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000244928 (Chr19:6251706..6251863 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATGAAGAAGACGCCCAGTTC Chr19:6251718..6251737 59.29 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000244928 (Chr19:6251706..6251863 +)
Downstram Exon
ENSMUSE00000244920 (Chr19:6252427..6252577 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATGAAGAAGACGCCCAGTTC Chr19:6251718..6251737 59.29 50 GGTACTGGGCTACGCTGAAG Chr19:6252517..6252536 59.9 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000468095 Chr19:6241668..6241966 GTGTGAAAGAGCGTGTCTGC Chr19:6241827..6241846 59.63 55
upstream ENSMUSE00000471193 Chr19:6244427..6244589 GCTGCACTTCTCACTGACCA Chr19:6244514..6244533 60.19 55
upstream ENSMUSE00000470176 Chr19:6244687..6244839 CTCTCAGAGTTGGGCCTCAT Chr19:6244703..6244722 59.4 55
upstream ENSMUSE00000472274 Chr19:6245046..6245148 TGATGAGGATCGAAGTGTGG Chr19:6245107..6245126 59.63 50
upstream ENSMUSE00000341878 Chr19:6245459..6245693 GTACGTGGAGCTCATGGTGA Chr19:6245639..6245658 59.71 55
upstream ENSMUSE00000245386 Chr19:6246304..6246400 TGGAGGTATCAGGACAACTGG Chr19:6246305..6246325 59.97 52.38
upstream ENSMUSE00000245213 Chr19:6246488..6246649 TGAGGACTTGTGGCTCATTG Chr19:6246537..6246556 59.83 50
upstream ENSMUSE00000245182 Chr19:6246752..6246892 GTGACATCGGCTGTCTCTGA Chr19:6246787..6246806 59.99 55
upstream ENSMUSE00000245155 Chr19:6247639..6247876 TTTTGCTGAGTTCGATGCTG Chr19:6247775..6247794 60.13 45
upstream ENSMUSE00000245124 Chr19:6247963..6248110 CACTTTGGACAGCTGGAGGT Chr19:6248042..6248061 60.3 55
upstream ENSMUSE00000245097 Chr19:6248197..6248289 CTGAGCTTCCCCAGTCACTC Chr19:6248200..6248219 59.99 60
upstream ENSMUSE00000245064 Chr19:6249772..6249927 CTTGTTCCGTCAAGTCACCA Chr19:6249879..6249898 59.72 50
upstream ENSMUSE00000245031 Chr19:6250024..6250267 GCTGCAGACAGTGTTTCGTC Chr19:6250047..6250066 59.63 55
upstream ENSMUSE00000245000 Chr19:6250413..6250509 AGGAGCACTGAGGCCAAGTA Chr19:6250478..6250497 60.01 55
upstream ENSMUSE00000244978 Chr19:6250596..6250755 GTCCGTGTGAGCTACAGCAA Chr19:6250685..6250704 60.06 55
upstream ENSMUSE00000244963 Chr19:6251259..6251401 ACTGTCCCGCTGTACTCTGG Chr19:6251315..6251334 60.32 60
upstream ENSMUSE00000244946 Chr19:6251488..6251603 TCTTCGGGGTTCAAGATGTG Chr19:6251564..6251583 61.03 50
upstream ENSMUSE00000244928 Chr19:6251706..6251863 ATGAAGAAGACGCCCAGTTC Chr19:6251718..6251737 59.29 50

*** Putative Vector Insertion (Chr 19: 6251864 - 6252426) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000244920 Chr19:6252427..6252577 GGTACTGGGCTACGCTGAAG Chr19:6252517..6252536 59.9 60
downstream ENSMUSE00000519567 Chr19:6252690..6252883 GTCCAGGTGGATACGGACAG Chr19:6252868..6252887 60.39 60
downstream ENSMUSE00000244890 Chr19:6252988..6253068 CAGCCGTACTGTCACCAAAA Chr19:6253014..6253033 59.76 50
downstream ENSMUSE00000244878 Chr19:6253334..6253440 CAGGACAGTGATGACGGTTG Chr19:6253408..6253427 60.15 55
downstream ENSMUSE00000244862 Chr19:6253524..6253616 GAGGGTGAAGGTCTCAGCAG Chr19:6253578..6253597 59.99 60
downstream ENSMUSE00000244824 Chr19:6254359..6254429 ACAGAGCGGAGTCATCAAGG Chr19:6254387..6254406 60.41 55
downstream ENSMUSE00000244795 Chr19:6254590..6254666 CCCTTCCAGGTTTTGATGAC Chr19:6254650..6254669 59.38 50
downstream ENSMUSE00000417223 Chr19:6255101..6255265 CCCGAGCTGGTTAGGTACTG Chr19:6255213..6255232 59.75 60
downstream ENSMUSE00000421446 Chr19:6255409..6255538 TATCCAGAAGGGCGTCAGTC Chr19:6255502..6255521 60.22 55
downstream ENSMUSE00000421440 Chr19:6255619..6255827 ATAGACGGAGACGGGAGAGG Chr19:6255659..6255678 60.61 60
downstream ENSMUSE00000144884 Chr19:6256168..6256376 GTAGTACCACACGGCTGCTG Chr19:6256315..6256334 59.39 60
downstream ENSMUSE00000144879 Chr19:6256552..6256687 CCTGTGAGGCCTACTCTTGC Chr19:6256575..6256594 60.01 60
downstream ENSMUSE00000144890 Chr19:6257439..6257642 CAGCTATGGCCGACTCTTCT Chr19:6257487..6257506 59.6 55
downstream ENSMUSE00000144878 Chr19:6257777..6257878 AGGCATCATGGAGACTCGAA Chr19:6257860..6257879 60.77 50
downstream ENSMUSE00000144888 Chr19:6257963..6258044 GGACCATGGGGTTGATACTG Chr19:6258029..6258048 60.05 55
downstream ENSMUSE00000353038 Chr19:6258134..6258266 GATAGGCTGCTGGTCAGAGG Chr19:6258261..6258280 59.97 60
downstream ENSMUSE00000244604 Chr19:6258361..6258433 ATGGTAATCCAGGCAGATGG Chr19:6258409..6258428 59.77 50
downstream ENSMUSE00000144886 Chr19:6258551..6258633 CAGCAGAGCCTCTTGAGCTT Chr19:6258627..6258646 60.03 55
downstream ENSMUSE00000144889 Chr19:6258864..6258985 TCATTGAGGGCATAGCACAG Chr19:6258908..6258927 59.82 50
downstream ENSMUSE00000245607 Chr19:6259989..6260143 CTGTGGATGACCCAAAGGAG Chr19:6260099..6260118 60.5 55
downstream ENSMUSE00000421388 Chr19:6261372..6261524 CTTGTAGGGATCGGGAGACA Chr19:6261438..6261457 60.06 55
downstream ENSMUSE00000245575 Chr19:6261601..6262304 CTTCACAGTGGCCATCCTTT Chr19:6261984..6262003 60.11 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGTGAGCTTCCAACTCCAGA Chr19:6251884..6251904 60.39 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTGAGCTTCCAACTCCAGA Chr19:6251884..6251904 60.39 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000024773