Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31039
Trapped Gene
2210408I21Rik (ENSMUSG00000071252)
Vector Insertion
Chr 13: 77384624 - 77393383
Public Clones IST14154C12 (tigm) IST10528H3 (tigm) IST13735E11 (tigm) IST14257B11 (tigm)
IST10320H9 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 31% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000612590 (Chr13:77384462..77384623 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTCAGATGCCCAGGAGTTCT Chr13:77384600..77384619 59.8 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000612590 (Chr13:77384462..77384623 +)
Downstram Exon
ENSMUSE00000612589 (Chr13:77393384..77393478 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTCAGATGCCCAGGAGTTCT Chr13:77384600..77384619 59.8 50 TGCCTCTGGTGGTTTATTGTT Chr13:77393462..77393482 59.49 42.86

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000119318 Chr13:77274860..77274891 No primer for this exon
upstream ENSMUSE00000612592 Chr13:77314114..77314245 GTTTCCCGGAGATTTGGAGT Chr13:77314174..77314193 60.31 50
upstream ENSMUSE00000612591 Chr13:77322862..77323030 CCAGATGCACAGCTACAAACA Chr13:77322911..77322931 59.92 47.62
upstream ENSMUSE00000570090 Chr13:77331815..77332484 CAAGCAAGAGCTGCAACAAG Chr13:77332440..77332459 59.93 50
upstream ENSMUSE00000612590 Chr13:77384462..77384623 TTCAGATGCCCAGGAGTTCT Chr13:77384600..77384619 59.8 50

*** Putative Vector Insertion (Chr 13: 77384624 - 77393383) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000612589 Chr13:77393384..77393478 TGCCTCTGGTGGTTTATTGTT Chr13:77393462..77393482 59.49 42.86
downstream ENSMUSE00000612588 Chr13:77399102..77399329 ATGCAGTGTGCTATGGCAAG Chr13:77399172..77399191 59.9 50
downstream ENSMUSE00000612587 Chr13:77401150..77401415 CGCTGAGAGACATACGTTGC Chr13:77401376..77401395 59.62 55
downstream ENSMUSE00000612586 Chr13:77402793..77402943 GAATTCCTGATAGCGCTGGA Chr13:77402835..77402854 60.32 50
downstream ENSMUSE00000612585 Chr13:77406923..77407113 AGCTTAGGGGGCAGTATGGT Chr13:77407014..77407033 59.98 55
downstream ENSMUSE00000612584 Chr13:77409023..77409205 No primer for this exon
downstream ENSMUSE00000612583 Chr13:77420303..77420413 GTGATTCATCGACACCATGC Chr13:77420334..77420353 59.93 50
downstream ENSMUSE00000612582 Chr13:77437728..77437867 GGCTGCGATAAGAGCAGTTT Chr13:77437790..77437809 59.62 50
downstream ENSMUSE00000612579 Chr13:77442557..77442721 CAGGCTACCACCTGCACTCT Chr13:77442606..77442625 60.47 60
downstream ENSMUSE00000612544 Chr13:77455609..77455833 GTCCATCAGTGCCAGTCTCA Chr13:77455673..77455692 59.83 55
downstream ENSMUSE00000612543 Chr13:77462626..77463031 AAGCTGTTGCTCCATCCAGT Chr13:77463005..77463024 59.87 50
downstream ENSMUSE00000612542 Chr13:77467128..77467284 GGACCATCGCATTTGTTTTC Chr13:77467216..77467235 60.32 45
downstream ENSMUSE00000612541 Chr13:77471564..77471719 AGGCTGATCTTCATCCCTCA Chr13:77471665..77471684 59.76 50
downstream ENSMUSE00000612540 Chr13:77473530..77473638 ATTTGGCAGCAAGTTTGACC Chr13:77473580..77473599 60.12 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGACTGCTTAATCGCCTTGC Chr13:77387667..77387687 59.62 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTCAGATGCCCAGGAGTTCT Chr13:77387601..77387621 59.8 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000071252