Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25019
Trapped Gene
Itga9 (ENSMUSG00000039115)
Vector Insertion
Chr 9: 118759925 - 118778408
Public Clones IST14314B12 (tigm) IST10037D3 (tigm) IST11063C6 (tigm) IST11063C6 (tigm)
IST10046A8 (tigm) IST12101F9 (tigm) IST12102F8 (tigm) IST14725A7 (tigm)
IST14996E6 (tigm) IST12102F8 (tigm) IST14996E6 (tigm)
Private Clones OST197971 (lexicon) OST68065 (lexicon) OST50578 (lexicon)
Severity of mutation (?) Insertion after 82% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000271559 (Chr9:118759817..118759924 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACCCTTCCTGGGTCATCTGT Chr9:118759838..118759857 60.77 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000271559 (Chr9:118759817..118759924 +)
Downstram Exon
ENSMUSE00000385100 (Chr9:118778409..118778534 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACCCTTCCTGGGTCATCTGT Chr9:118759838..118759857 60.77 55 GGGGTCGGGTTTCTTTGTAG Chr9:118778458..118778477 60.71 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000396297 Chr9:118515827..118516233 GAGCACTTCCACGACAACAC Chr9:118516208..118516227 59.31 55
upstream ENSMUSE00000347873 Chr9:118535566..118535693 GCACCGAAGGCAGATTCTAA Chr9:118535579..118535598 60.35 50
upstream ENSMUSE00000393911 Chr9:118537257..118537363 No primer for this exon
upstream ENSMUSE00000348460 Chr9:118545621..118545744 CCCATCGTTGGAAGAACATC Chr9:118545628..118545647 60.32 50
upstream ENSMUSE00000449613 Chr9:118561615..118561682 CGGAATAGCAGGCTTCTTCA Chr9:118561658..118561677 60.48 50
upstream ENSMUSE00000401364 Chr9:118567584..118567713 GTTTTATTGGGCTGGGACAC Chr9:118567613..118567632 59.29 50
upstream ENSMUSE00000353237 Chr9:118570466..118570551 ACAGGATGAAGGCATTGGAA Chr9:118570530..118570549 60.46 45
upstream ENSMUSE00000385327 Chr9:118572988..118573056 AGAGCTGACCGAAGATCAGG Chr9:118573000..118573019 59.56 55
upstream ENSMUSE00000467483 Chr9:118577730..118577867 CCGTCTACCTCAACCAAGGA Chr9:118577845..118577864 60.1 55
upstream ENSMUSE00000350361 Chr9:118580817..118580922 CTGACCCTGACTGGAGATGC Chr9:118580835..118580854 60.83 60
upstream ENSMUSE00000396224 Chr9:118581928..118582022 GGCACCTAAGGAGGAGGACT Chr9:118581941..118581960 59.7 60
upstream ENSMUSE00000390595 Chr9:118590054..118590144 GTCTGGGAGGAGGCTAAACC Chr9:118590059..118590078 60.07 60
upstream ENSMUSE00000350169 Chr9:118590853..118590898 No primer for this exon
upstream ENSMUSE00000384699 Chr9:118598388..118598542 GTGTCACGATGGACAACAGC Chr9:118598457..118598476 60.17 55
upstream ENSMUSE00000343874 Chr9:118607432..118607592 CCACATGGACGAAGTGTGTC Chr9:118607550..118607569 60.01 55
upstream ENSMUSE00000379721 Chr9:118678210..118678359 ATTGTGTTTGAAGCCGCCTA Chr9:118678237..118678256 60.64 45
upstream ENSMUSE00000346515 Chr9:118693220..118693296 TTGCCAATCTGAGGACTGTG Chr9:118693237..118693256 59.83 50
upstream ENSMUSE00000379199 Chr9:118716283..118716433 TGATGCCAACGTGTCCTTTA Chr9:118716373..118716392 60.11 45
upstream ENSMUSE00000271638 Chr9:118741852..118741938 GTGCAGTGTGGGATTTCCTT Chr9:118741899..118741918 59.97 50
upstream ENSMUSE00000271624 Chr9:118743414..118743493 AGCTTCATCGTGACTGCTCA Chr9:118743471..118743490 59.73 50
upstream ENSMUSE00000271604 Chr9:118750211..118750300 AGTGGACACGTCCATCACTG Chr9:118750280..118750299 59.58 55
upstream ENSMUSE00000271583 Chr9:118752607..118752715 CCTTCGTGTATGGCGAGTCT Chr9:118752624..118752643 60.28 55
upstream ENSMUSE00000271559 Chr9:118759817..118759924 ACCCTTCCTGGGTCATCTGT Chr9:118759838..118759857 60.77 55

*** Putative Vector Insertion (Chr 9: 118759925 - 118778408) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000385100 Chr9:118778409..118778534 GGGGTCGGGTTTCTTTGTAG Chr9:118778458..118778477 60.71 55
downstream ENSMUSE00000344626 Chr9:118780939..118781058 CGGAAGAGCACTAAGGTTGC Chr9:118781001..118781020 60.01 55
downstream ENSMUSE00000382743 Chr9:118786240..118786341 GAGCCATGAACTGGATGACA Chr9:118786273..118786292 59.64 50
downstream ENSMUSE00000352694 Chr9:118796882..118797001 AGCAAACTGATGGCGATGAT Chr9:118796958..118796977 60.63 45
downstream ENSMUSE00000395328 Chr9:118806352..118808057 GCAACTGCTGAGAGGAAACC Chr9:118807202..118807221 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCCATGCAAAGCACATTCTA Chr9:118759892..118759912 59.69 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCCATGCAAAGCACATTCTA Chr9:118759892..118759912 59.69 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039115