Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7078
Trapped Gene
Jmjd1c (ENSMUSG00000037876)
Vector Insertion
Chr 10: 66686930 - 66687484
Public Clones RRZ026 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 38% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000575819 (Chr10:66686757..66686929 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTGACCTCAGCGGATGGTAT Chr10:66686793..66686812 59.96 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000575819 (Chr10:66686757..66686929 +)
Downstram Exon
ENSMUSE00000371587 (Chr10:66687485..66689667 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTGACCTCAGCGGATGGTAT Chr10:66686793..66686812 59.96 55 AAGGGTGTAGAGGCCGAAAT Chr10:66688882..66688901 59.96 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000419774 Chr10:66648728..66649059 TGCTTCGTTCTGTGGTCTTG Chr10:66648813..66648832 60.03 50
upstream ENSMUSE00000642903 Chr10:66652484..66652597 GTGCCTTTCAGCCATACCAG Chr10:66652578..66652597 60.66 55
upstream ENSMUSE00000642902 Chr10:66678018..66678123 GCTTAAAGCCCGTACTCAGG Chr10:66678031..66678050 59 55
upstream ENSMUSE00000642884 Chr10:66679731..66679855 CGCACCATGATCGTTATGAA Chr10:66679829..66679848 60.49 45
upstream ENSMUSE00000289838 Chr10:66680786..66680929 ATTACATCACGGCGAAGGTC Chr10:66680879..66680898 59.96 50
upstream ENSMUSE00000289832 Chr10:66681025..66681217 CCAGCAACAGCAACAAAGAA Chr10:66681105..66681124 60.03 45
upstream ENSMUSE00000575821 Chr10:66681702..66683383 TGGAGTGCCTACTGCCTCTT Chr10:66683092..66683111 60.01 55
upstream ENSMUSE00000575819 Chr10:66686757..66686929 GTGACCTCAGCGGATGGTAT Chr10:66686793..66686812 59.96 55

*** Putative Vector Insertion (Chr 10: 66686930 - 66687484) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000371587 Chr10:66687485..66689667 AAGGGTGTAGAGGCCGAAAT Chr10:66688882..66688901 59.96 50
downstream ENSMUSE00000289729 Chr10:66692596..66692797 AAGTCTGCACTCTCGGCACT Chr10:66692732..66692751 60.21 55
downstream ENSMUSE00000289722 Chr10:66694720..66694934 CAACGCTGTTTTCTCAGACG Chr10:66694918..66694937 59.63 50
downstream ENSMUSE00000289712 Chr10:66696119..66696271 GTGGACGTTGAACAGTGTGG Chr10:66696201..66696220 60.05 55
downstream ENSMUSE00000289707 Chr10:66700856..66700945 GCTGGCCTTTCACACACTTC Chr10:66700900..66700919 60.84 55
downstream ENSMUSE00000289699 Chr10:66701555..66701682 AAGAATGTGCATGGCATCAA Chr10:66701592..66701611 60.08 40
downstream ENSMUSE00000289693 Chr10:66701997..66702207 CTTGCACTTCCAGGGCTACT Chr10:66702118..66702137 59.5 55
downstream ENSMUSE00000666227 Chr10:66701997..66702177 CTTGCACTTCCAGGGCTACT Chr10:66702118..66702137 59.5 55
downstream ENSMUSE00000575817 Chr10:66702610..66702824 TGGTCAGCAAATCACGTAGG Chr10:66702750..66702769 59.72 50
downstream ENSMUSE00000289677 Chr10:66703411..66703689 TGCTGGTCACAGATCCAAGA Chr10:66703619..66703638 60.4 50
downstream ENSMUSE00000289672 Chr10:66706520..66706688 CTCCTTAACGTTGGCATTGG Chr10:66706663..66706682 60.49 50
downstream ENSMUSE00000289662 Chr10:66707531..66707621 CTTGAAGTCCTCCCCAGATG Chr10:66707607..66707626 59.65 55
downstream ENSMUSE00000289657 Chr10:66708254..66708384 ACAAAGAACCCTGGCAAATG Chr10:66708349..66708368 59.97 45
downstream ENSMUSE00000666226 Chr10:66708361..66708384 No primer for this exon
downstream ENSMUSE00000289650 Chr10:66708782..66708904 AGAGGACGCCATTTCCTTTT Chr10:66708898..66708917 60.07 45
downstream ENSMUSE00000289640 Chr10:66710759..66710898 CACCAGGGATTTCACTCGAA Chr10:66710842..66710861 61.03 50
downstream ENSMUSE00000289631 Chr10:66712378..66712554 GTCTCTGGCGGAGCTTTCTA Chr10:66712471..66712490 59.72 55
downstream ENSMUSE00000612311 Chr10:66717200..66717331 TCTTCGGTCACCTGAACACA Chr10:66717240..66717259 60.28 50
downstream ENSMUSE00000642890 Chr10:66718196..66719066 CCAACCGCAATTAGGTGTCT Chr10:66718298..66718317 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCCCCACTGACAAAGACATT Chr10:66686893..66686913 59.82 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCCCCACTGACAAAGACATT Chr10:66686893..66686913 59.82 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037876