Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2476
Trapped Gene
Bdp1 (ENSMUSG00000049658)
Vector Insertion
Chr 13: 100805795 - 100807714
Public Clones XT0660 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 39% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000293546 (Chr13:100807715..100807892 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGACACTCGATTCGGGTCAG Chr13:100807796..100807815 60.26 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000293546 (Chr13:100807715..100807892 -)
Downstram Exon
ENSMUSE00000293536 (Chr13:100805734..100805794 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGACACTCGATTCGGGTCAG Chr13:100807796..100807815 60.26 55 TTGAGGACCGGTGTTTTCTT Chr13:100805722..100805741 59.57 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000293416 Chr13:100845460..100845576 TTGCAGGTTTAGCACCCAGT Chr13:100845501..100845520 60.69 50
upstream ENSMUSE00000293410 Chr13:100844342..100844500 CATGCCACTAGCAAGGGAGT Chr13:100844466..100844485 60.28 55
upstream ENSMUSE00000293404 Chr13:100840032..100840191 GCAGTTGGGAAGAAATCAGC Chr13:100840096..100840115 59.82 50
upstream ENSMUSE00000293396 Chr13:100837420..100837511 GGTGCCAAAACTGTGTCTGA Chr13:100837420..100837439 59.73 50
upstream ENSMUSE00000293390 Chr13:100835832..100836021 TGAGGAGTCGAATGCAAAGA Chr13:100835937..100835956 59.52 45
upstream ENSMUSE00000293381 Chr13:100834314..100834444 TCAGCCCCAGGTTCTTAGTG Chr13:100834324..100834343 60.25 55
upstream ENSMUSE00000569404 Chr13:100830249..100831461 TGTTGCTCCAAGAGAACGTG Chr13:100830338..100830357 60.03 50
upstream ENSMUSE00000611201 Chr13:100829444..100829625 CCAGCCACTTAGGTCATGTG Chr13:100829536..100829555 59.16 55
upstream ENSMUSE00000611200 Chr13:100828681..100828900 CAAGAACAGCAGCCACTTCA Chr13:100828868..100828887 60.17 50
upstream ENSMUSE00000611199 Chr13:100826114..100826295 CTTCACCGCCAAATTCAAGT Chr13:100826176..100826195 60.11 45
upstream ENSMUSE00000611198 Chr13:100825051..100825258 GTGAGGGGTCGACTTCAGAG Chr13:100825175..100825194 59.83 60
upstream ENSMUSE00000611197 Chr13:100822928..100823073 TGTCAGAGTGCCAAGTGAGTG Chr13:100823001..100823021 60.08 52.38
upstream ENSMUSE00000611196 Chr13:100821303..100821510 CTGATAAGAAGGCGGTTCCA Chr13:100821454..100821473 60.21 50
upstream ENSMUSE00000611195 Chr13:100820900..100821084 GGGATGAGACTGCGAAAGAG Chr13:100820950..100820969 59.95 55
upstream ENSMUSE00000611194 Chr13:100819591..100819984 CCTATCATCTTGCCCCAGAA Chr13:100819678..100819697 60.03 50
upstream ENSMUSE00000611193 Chr13:100816681..100816794 AAAGCTGTGTATCCGCCATC Chr13:100816685..100816704 60.1 50
upstream ENSMUSE00000611192 Chr13:100814227..100814263 No primer for this exon
upstream ENSMUSE00000611191 Chr13:100813714..100813806 GGAAGCCGCCATAACTTTAC Chr13:100813768..100813787 58.72 50
upstream ENSMUSE00000680074 Chr13:100812380..100812386 No primer for this exon
upstream ENSMUSE00000293575 Chr13:100812015..100812240 TATCCGGAGGTTTGTTCACC Chr13:100812129..100812148 59.79 50
upstream ENSMUSE00000293567 Chr13:100811377..100811537 TCATCAGGAAGTTGCCAGTTT Chr13:100811415..100811435 59.73 42.86
upstream ENSMUSE00000293557 Chr13:100808077..100808227 AAGAGGAGCAGTCGCAGTGT Chr13:100808130..100808149 60.21 55
upstream ENSMUSE00000680073 Chr13:100808077..100808233 AAGAGGAGCAGTCGCAGTGT Chr13:100808130..100808149 60.21 55
upstream ENSMUSE00000293546 Chr13:100807715..100807892 AGACACTCGATTCGGGTCAG Chr13:100807796..100807815 60.26 55

*** Putative Vector Insertion (Chr 13: 100805795 - 100807714) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000293536 Chr13:100805734..100805794 TTGAGGACCGGTGTTTTCTT Chr13:100805722..100805741 59.57 45
downstream ENSMUSE00000293527 Chr13:100805039..100805225 GCAGAGAGCTCGGCATTAAC Chr13:100805072..100805091 60.12 55
downstream ENSMUSE00000293516 Chr13:100800740..100800944 GTGAGGACTTTTTGGCAGGA Chr13:100800756..100800775 60.23 50
downstream ENSMUSE00000293508 Chr13:100797390..100797426 No primer for this exon
downstream ENSMUSE00000371885 Chr13:100795352..100795610 TTGTCCCATGCAAGACTCTG Chr13:100795569..100795588 59.83 50
downstream ENSMUSE00000293491 Chr13:100793555..100793810 AAATTTCGCCGTGATACAGG Chr13:100793660..100793679 59.96 45
downstream ENSMUSE00000359807 Chr13:100787952..100790365 TCACCTCTTCCTCAGGTGCT Chr13:100790271..100790290 59.99 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGGCCAGAGGTAAAGCAATG Chr13:100807702..100807722 61.88 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGGCCAGAGGTAAAGCAATG Chr13:100807702..100807722 61.88 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000049658