Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2177
Trapped Gene
Dnajc17 (ENSMUSG00000034278)
Vector Insertion
Chr 2: 119012152 - 119034423
Public Clones XS0674 (sanger) RRH136 (baygenomics) XK733 (baygenomics) IST12001A10 (tigm)
IST10071C9BBF1 (tigm) IST14721E4 (tigm) IST10919F3 (tigm) IST14947B8 (tigm)
IST14947B9 (tigm)
Private Clones OST352650 (lexicon) OST260506 (lexicon)
Severity of mutation (?) Insertion after 8% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000307758 (Chr2:119034424..119034510 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACTAGAACCATGGCGGTGAC Chr2:119034491..119034510 60 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000307758 (Chr2:119034424..119034510 -)
Downstram Exon
ENSMUSE00000307752 (Chr2:119012082..119012151 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACTAGAACCATGGCGGTGAC Chr2:119034491..119034510 60 55 GGCAGGATAGTGCTTTTTGC Chr2:119012093..119012112 59.85 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000307758 Chr2:119034424..119034510 ACTAGAACCATGGCGGTGAC Chr2:119034491..119034510 60 55

*** Putative Vector Insertion (Chr 2: 119012152 - 119034423) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000307752 Chr2:119012082..119012151 GGCAGGATAGTGCTTTTTGC Chr2:119012093..119012112 59.85 50
downstream ENSMUSE00000307747 Chr2:119011765..119011823 GGACAGCTGGTGGAAGAGTT Chr2:119011779..119011798 59.31 55
downstream ENSMUSE00000307739 Chr2:119011432..119011519 CGTCAAGTCTCTGGGTCCTC Chr2:119011434..119011453 59.83 60
downstream ENSMUSE00000307729 Chr2:119009653..119009738 GCTCCTGCTCTCCTCCTCTT Chr2:119009652..119009671 60.24 60
downstream ENSMUSE00000307719 Chr2:119009335..119009431 ACTGACGGGAACCCTCTTCT Chr2:119009376..119009395 60.11 55
downstream ENSMUSE00000307708 Chr2:119006662..119006705 GGGTTCCTTTGCCTTCAGTA Chr2:119006651..119006670 59.17 50
downstream ENSMUSE00000307697 Chr2:119006223..119006300 CTCTGGAGTAGCCACCTTGG Chr2:119006227..119006246 59.86 60
downstream ENSMUSE00000307689 Chr2:119005621..119005701 CATTGCCTGCCTTCTTTCTG Chr2:119005631..119005650 60.9 50
downstream ENSMUSE00000307679 Chr2:119005088..119005198 CTCCAACCAGGAAACCTTCA Chr2:119005114..119005133 60.08 50
downstream ENSMUSE00000384836 Chr2:118998243..118998421 TCCCTTTCTGACAGCACTGA Chr2:118998377..118998396 59.54 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTTAGGAGCCTGAGTCCAA Chr2:119034398..119034418 59.57 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTATCATTCCCACCGCTGAT Chr2:119034404..119034424 60.3 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 ACTCTGCCATAATCGCCTTG Chr2:119034449..119034469 60.24 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TGTTCTTCGTGACTGGGAAA Chr2:119034447..119034467 59.26 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034278