Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI15948
Trapped Gene
Ssbp3 (ENSMUSG00000061887)
Vector Insertion
Chr 4: 106622151 - 106682283
Public Clones IST12584B9 (tigm) IST12351B2 (tigm) IST12840G1 (tigm) IST12845E4 (tigm)
IST14537G6 (tigm) IST10324A7 (tigm) IST14841E5 (tigm)
Private Clones OST469524 (lexicon) OST441317 (lexicon) OST374676 (lexicon) OST364159 (lexicon)
OST277558 (lexicon) OST147842 (lexicon) OST55774 (lexicon) OST378 (lexicon)
Severity of mutation (?) Insertion after 10% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000631626 (Chr4:106622061..106622150 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCAGGCTGTGTGGTTTTCTC Chr4:106622081..106622100 60.84 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000631626 (Chr4:106622061..106622150 +)
Downstram Exon
ENSMUSE00000180685 (Chr4:106682284..106682373 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCAGGCTGTGTGGTTTTCTC Chr4:106622081..106622100 60.84 55 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000671094 Chr4:106584075..106584517 TTCGGTTGAGCTCCAAGTAGA Chr4:106584082..106584102 60 47.62
upstream ENSMUSE00000180677 Chr4:106585508..106585580 CTGCACGTAGGAGCACAGAA Chr4:106585536..106585555 60.2 55
upstream ENSMUSE00000525680 Chr4:106585810..106585871 No primer for this exon
upstream ENSMUSE00000525679 Chr4:106588250..106588334 ACTGTGCAGCTCCTGAAAGG Chr4:106588267..106588286 60.59 55
upstream ENSMUSE00000631626 Chr4:106622061..106622150 GCAGGCTGTGTGGTTTTCTC Chr4:106622081..106622100 60.84 55

*** Putative Vector Insertion (Chr 4: 106622151 - 106682283) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000180685 Chr4:106682284..106682373 No primer for this exon
downstream ENSMUSE00000477019 Chr4:106699822..106699902 GATTGTGAGGTGGAGGCTGT Chr4:106699876..106699895 60.12 55
downstream ENSMUSE00000525678 Chr4:106700798..106700857 GCATATCGCGGTGACATAAA Chr4:106700823..106700842 59.55 45
downstream ENSMUSE00000358806 Chr4:106703467..106703533 GTGTGGGATCCATGGAATTG Chr4:106703527..106703546 60.99 50
downstream ENSMUSE00000399590 Chr4:106703620..106703696 CTGCATTGATCCTCCCATGT Chr4:106703651..106703670 60.89 50
downstream ENSMUSE00000180691 Chr4:106709541..106709605 GAGTTGGGTGGTGGTCTCAT Chr4:106709578..106709597 59.82 55
downstream ENSMUSE00000180690 Chr4:106710207..106710255 TGAGTTAGCACTGTTGGGATTG Chr4:106710256..106710277 60.17 45.46
downstream ENSMUSE00000377201 Chr4:106710827..106710862 ACATAGGTTCCGGGTGATGA Chr4:106710864..106710883 60.19 50
downstream ENSMUSE00000710291 Chr4:106711331..106711385 ACTAGGCATGATGGGGGTTC Chr4:106711381..106711400 61.11 55
downstream ENSMUSE00000711216 Chr4:106711331..106711385 ACTAGGCATGATGGGGGTTC Chr4:106711381..106711400 61.11 55
downstream ENSMUSE00000370641 Chr4:106712568..106712638 No primer for this exon
downstream ENSMUSE00000671055 Chr4:106712568..106712638 No primer for this exon
downstream ENSMUSE00000341955 Chr4:106718921..106718999 AGGGATCCATTCATGTGGTG Chr4:106719000..106719019 60.6 50
downstream ENSMUSE00000671054 Chr4:106718921..106718999 AGGGATCCATTCATGTGGTG Chr4:106719000..106719019 60.6 50
downstream ENSMUSE00000382392 Chr4:106719847..106719875 No primer for this exon
downstream ENSMUSE00000671051 Chr4:106719847..106719875 No primer for this exon
downstream ENSMUSE00000396373 Chr4:106719969..106720070 GTCGTTCTGGAAGGAGTGGA Chr4:106720070..106720089 60.24 55
downstream ENSMUSE00000671047 Chr4:106719969..106720070 GTCGTTCTGGAAGGAGTGGA Chr4:106720070..106720089 60.24 55
downstream ENSMUSE00000471947 Chr4:106720629..106722298 AGCTGACACCTGCATCTCCT Chr4:106721411..106721430 60.02 55
downstream ENSMUSE00000631627 Chr4:106720629..106722298 AGCTGACACCTGCATCTCCT Chr4:106721411..106721430 60.02 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCATGTTGCAGGGGATACCT Chr4:106670183..106670203 60.34 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGGTAGCTGTCCTCAGTTCCTG Chr4:106679142..106679164 59.94 54.54 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000061887