Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI19610
Trapped Gene
Atxn7l2 (ENSMUSG00000048997)
Vector Insertion
Chr 3: 108009227 - 108009740
Public Clones not available
Private Clones OST386148 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000709918 (Chr3:108009741..108009931 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TAAAACCCACCGAAAGATGG Chr3:108009744..108009763 59.79 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000709918 (Chr3:108009741..108009931 -)
Downstram Exon
ENSMUSE00000361424 (Chr3:108009144..108009226 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TAAAACCCACCGAAAGATGG Chr3:108009744..108009763 59.79 45 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000662148 Chr3:108013263..108013852 CGGGTATGCGCAGTAAGTTT Chr3:108013714..108013733 60.15 50
upstream ENSMUSE00000709590 Chr3:108013263..108013380 No primer for this exon
upstream ENSMUSE00000718411 Chr3:108013263..108013404 No primer for this exon
upstream ENSMUSE00000722322 Chr3:108013263..108013384 No primer for this exon
upstream ENSMUSE00000662147 Chr3:108011835..108012013 CTTGCGTAGCTGATCAAGGA Chr3:108011940..108011959 59.17 50
upstream ENSMUSE00000662146 Chr3:108011358..108011423 AGAAACTTGACGCCATGACC Chr3:108011371..108011390 60.12 50
upstream ENSMUSE00000717041 Chr3:108011358..108011423 AGAAACTTGACGCCATGACC Chr3:108011371..108011390 60.12 50
upstream ENSMUSE00000636612 Chr3:108010881..108011185 AGGGAAATCCGGAGAATTTG Chr3:108011017..108011036 60.26 45
upstream ENSMUSE00000662145 Chr3:108010881..108010985 GTAACCACTGCAGCCAGGTG Chr3:108010912..108010931 61.71 60
upstream ENSMUSE00000391128 Chr3:108010312..108010522 AGGTTCCACCAAAACCTCCT Chr3:108010385..108010404 59.83 50
upstream ENSMUSE00000636611 Chr3:108010312..108010522 AGGTTCCACCAAAACCTCCT Chr3:108010385..108010404 59.83 50
upstream ENSMUSE00000402522 Chr3:108009741..108010027 TAAAACCCACCGAAAGATGG Chr3:108009744..108009763 59.79 45
upstream ENSMUSE00000709918 Chr3:108009741..108009931 TAAAACCCACCGAAAGATGG Chr3:108009744..108009763 59.79 45

*** Putative Vector Insertion (Chr 3: 108009227 - 108009740) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000361424 Chr3:108009144..108009226 No primer for this exon
downstream ENSMUSE00000564956 Chr3:108009144..108010027 AGGTTCCAATGAATCGCAAG Chr3:108009218..108009237 60.07 45
downstream ENSMUSE00000414713 Chr3:108008550..108008803 AGTTCGGCCACTAGCACATC Chr3:108008711..108008730 60.28 55
downstream ENSMUSE00000564955 Chr3:108008543..108008803 AGTTCGGCCACTAGCACATC Chr3:108008711..108008730 60.28 55
downstream ENSMUSE00000363852 Chr3:108007634..108007832 ACCTTCGTCATCCACCTCAC Chr3:108007771..108007790 59.97 55
downstream ENSMUSE00000375239 Chr3:108007419..108007540 GGCGGCTAAACACATAGCAT Chr3:108007464..108007483 60.12 50
downstream ENSMUSE00000662144 Chr3:108006166..108006961 TGAGAAGCCTTGACGGGTAT Chr3:108006367..108006386 59.69 50
downstream ENSMUSE00000564953 Chr3:108006142..108006927 TGAGAAGCCTTGACGGGTAT Chr3:108006367..108006386 59.69 50
downstream ENSMUSE00000662143 Chr3:108005173..108005291 No primer for this exon
downstream ENSMUSE00000710169 Chr3:108005158..108005291 No primer for this exon
downstream ENSMUSE00000719683 Chr3:108005146..108005291 No primer for this exon
downstream ENSMUSE00000714774 Chr3:108005140..108005291 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACTTAATCGCCTTGCAGCAC Chr3:108009672..108009692 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAAAACCCACCGAAAGATGG Chr3:108009742..108009762 59.79 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048997