Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14471
Trapped Gene
Cc2d1b (ENSMUSG00000028582)
Vector Insertion
Chr 4: 108305909 - 108306127
Public Clones FHCRC-GT-S11-4A1 (fhcrc)
Private Clones not available
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000414759 (Chr4:108305776..108305908 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGCAGACGGTCACTGAGAAC Chr4:108305855..108305874 60.03 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000414759 (Chr4:108305776..108305908 +)
Downstram Exon
ENSMUSE00000670804 (Chr4:108306128..108306693 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGCAGACGGTCACTGAGAAC Chr4:108305855..108305874 60.03 55 CGAGTTCTCCCATCCCTACA Chr4:108306448..108306467 60.06 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000429264 Chr4:108292561..108292678 AGCTTCCTGTGGCTGTCTCC Chr4:108292578..108292597 61.92 60
upstream ENSMUSE00000354895 Chr4:108294117..108294199 GAAGGGCCCTAAGACCAGTG Chr4:108294154..108294173 61.01 60
upstream ENSMUSE00000390231 Chr4:108296056..108296200 GGGCTTTTTGTGGAGTTCAA Chr4:108296059..108296078 60.09 45
upstream ENSMUSE00000349400 Chr4:108297049..108297152 TGTATGCGAGATGTGGAGGA Chr4:108297090..108297109 60.22 50
upstream ENSMUSE00000401420 Chr4:108297451..108297609 CTGGGTGAGGATGAAGAAGC Chr4:108297469..108297488 59.8 55
upstream ENSMUSE00000269925 Chr4:108298013..108298138 No primer for this exon
upstream ENSMUSE00000180439 Chr4:108298260..108298419 AGAGCCATCAAGAACCCTGA Chr4:108298365..108298384 59.8 50
upstream ENSMUSE00000180447 Chr4:108298586..108298758 GCTGTTAGCCCGACAGAGAG Chr4:108298662..108298681 60.16 60
upstream ENSMUSE00000670803 Chr4:108298653..108298758 GCTGTTAGCCCGACAGAGAG Chr4:108298662..108298681 60.16 60
upstream ENSMUSE00000180433 Chr4:108298906..108298981 GTCCTAGAGGCCCTGGAAAA Chr4:108298918..108298937 60.57 55
upstream ENSMUSE00000670802 Chr4:108298906..108298981 GTCCTAGAGGCCCTGGAAAA Chr4:108298918..108298937 60.57 55
upstream ENSMUSE00000180445 Chr4:108299085..108299195 GTCCCCAGCAGTAGAGCAAA Chr4:108299137..108299156 60.4 55
upstream ENSMUSE00000670801 Chr4:108299085..108299195 GTCCCCAGCAGTAGAGCAAA Chr4:108299137..108299156 60.4 55
upstream ENSMUSE00000180435 Chr4:108299279..108299409 CAACAACAGTGCTGGATGCT Chr4:108299294..108299313 59.9 50
upstream ENSMUSE00000670800 Chr4:108299279..108299409 CAACAACAGTGCTGGATGCT Chr4:108299294..108299313 59.9 50
upstream ENSMUSE00000180446 Chr4:108299653..108299725 TTTGCCGAGTTACCTGTTCC Chr4:108299701..108299720 60.11 50
upstream ENSMUSE00000670799 Chr4:108299653..108300553 ATGCAGCCCTGGTAGATGAC Chr4:108299995..108300014 60.1 55
upstream ENSMUSE00000180427 Chr4:108299899..108300023 ATGCAGCCCTGGTAGATGAC Chr4:108299995..108300014 60.1 55
upstream ENSMUSE00000180436 Chr4:108300436..108300553 AGCGCAGACTCTGGTCTCTC Chr4:108300474..108300493 59.89 60
upstream ENSMUSE00000337905 Chr4:108300635..108300807 GAGGCTCGGAAACTGCAATA Chr4:108300658..108300677 60.35 50
upstream ENSMUSE00000670798 Chr4:108300635..108300807 GAGGCTCGGAAACTGCAATA Chr4:108300658..108300677 60.35 50
upstream ENSMUSE00000180443 Chr4:108301188..108301313 ACCATGAGGATCTGCGACTC Chr4:108301234..108301253 60.23 55
upstream ENSMUSE00000413652 Chr4:108302179..108302237 GTGCCTGCTATTCTCCAAGC Chr4:108302181..108302200 59.99 55
upstream ENSMUSE00000353345 Chr4:108302322..108302438 GAGGACCGAAAGAAACAGCTT Chr4:108302338..108302358 59.88 47.62
upstream ENSMUSE00000180444 Chr4:108302697..108302770 CAGAAATGCATCTGATCATCG Chr4:108302720..108302740 59.24 42.86
upstream ENSMUSE00000180429 Chr4:108302883..108302941 AGTGACTCCGGATGACTTGG Chr4:108302884..108302903 60.11 55
upstream ENSMUSE00000180431 Chr4:108303149..108303200 No primer for this exon
upstream ENSMUSE00000180423 Chr4:108304201..108304300 AACCACCGAGGCTTTAGGAG Chr4:108304236..108304255 60.62 55
upstream ENSMUSE00000180422 Chr4:108304440..108304530 TGAAATTGGAAAGGCTGGAG Chr4:108304481..108304500 60.18 45
upstream ENSMUSE00000414759 Chr4:108305776..108305908 TGCAGACGGTCACTGAGAAC Chr4:108305855..108305874 60.03 55

*** Putative Vector Insertion (Chr 4: 108305909 - 108306127) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000379640 Chr4:108306128..108306710 CGAGTTCTCCCATCCCTACA Chr4:108306448..108306467 60.06 55
downstream ENSMUSE00000670804 Chr4:108306128..108306693 CGAGTTCTCCCATCCCTACA Chr4:108306448..108306467 60.06 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCTGGGGAGAAAGCTAATCG Chr4:108305946..108305966 59.41 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGCCCTGCTAAAACTTCCTT Chr4:108305916..108305936 60.73 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028582