Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI30728
Trapped Gene
Cdc2l5 (ENSMUSG00000041297)
Vector Insertion
Chr 13: 17843504 - 17855109
Public Clones IST14307B3 (tigm) IST11684H7 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 52% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000325269 (Chr13:17854938..17855108 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGGTTTCCCAATTACAGCAA Chr13:17855043..17855062 59.8 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000325269 (Chr13:17854938..17855108 -)
Downstram Exon
ENSMUSE00000571715 (Chr13:17843505..17843694 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGGTTTCCCAATTACAGCAA Chr13:17855043..17855062 59.8 45 TAATCCAGGCCTTCCATGAG Chr13:17843546..17843565 60.03 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000438720 Chr13:17895272..17896836 TGGTGGAGTACGAGGATGTG Chr13:17896039..17896058 59.54 55
upstream ENSMUSE00000325294 Chr13:17864135..17864791 GCAGCATGTGGCTTTAGTGA Chr13:17864196..17864215 60.02 50
upstream ENSMUSE00000325285 Chr13:17858270..17858440 AACTCCGATGTCTGCTTGCT Chr13:17858371..17858390 60.02 50
upstream ENSMUSE00000571716 Chr13:17856788..17856927 AATATGTGGGCCTCGCTATG Chr13:17856908..17856927 59.94 50
upstream ENSMUSE00000325269 Chr13:17854938..17855108 GGGTTTCCCAATTACAGCAA Chr13:17855043..17855062 59.8 45
upstream ENSMUSE00000571715 Chr13:17843505..17843694 CTCATGGAAGGCCTGGATTA Chr13:17843568..17843587 60.03 50

*** Putative Vector Insertion (Chr 13: 17843504 - 17855109) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000325259 Chr13:17842091..17842147 CGAGCAAGTCCAAAATCTGC Chr13:17842090..17842109 60.91 50
downstream ENSMUSE00000571714 Chr13:17830925..17831026 TTCAGGTGGACGATACCACA Chr13:17830956..17830975 59.96 50
downstream ENSMUSE00000325249 Chr13:17830751..17830828 GTGCAAGTTCCTGGTTTGCT Chr13:17830745..17830764 60.3 50
downstream ENSMUSE00000348664 Chr13:17819901..17820017 TTAACTTCCGCCGATATTGC Chr13:17819895..17819914 60.06 45
downstream ENSMUSE00000325237 Chr13:17818954..17819085 TCTCGCAGGAACTCACACTG Chr13:17818962..17818981 60.18 55
downstream ENSMUSE00000401768 Chr13:17812922..17813127 TCCTAGGGGCTTTGATTGTG Chr13:17813002..17813021 60.07 50
downstream ENSMUSE00000363800 Chr13:17811190..17811639 TTCCACTTTAGGCTGGATGG Chr13:17811343..17811362 60.07 50
downstream ENSMUSE00000571705 Chr13:17807568..17810745 AACTGGTGGTGGTTCAGGAG Chr13:17810602..17810621 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAATAATCGCCTTGCAGCAC Chr13:17855041..17855061 61.69 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATGAAAAGGAGGGCGTGACT Chr13:17855051..17855071 61.02 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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