Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10157
Trapped Gene
Csnk2a1 (ENSMUSG00000074698)
Vector Insertion
Chr 2: 152089030 - 152098363
Public Clones XB659 (baygenomics) IST12071F3 (tigm) IST12770E5 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 53% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000681807 (Chr2:152088919..152089029 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTTACCATCCAGGCCAAGAG Chr2:152088950..152088969 60.07 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000681807 (Chr2:152088919..152089029 +)
Downstram Exon
ENSMUSE00000640038 (Chr2:152098364..152098465 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTTACCATCCAGGCCAAGAG Chr2:152088950..152088969 60.07 50 ACCCAAGCTCCACATATCCA Chr2:152098402..152098421 60.34 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000681813 Chr2:152052618..152052727 CCGCCATATTGTCTGTGTGA Chr2:152052665..152052684 60.54 50
upstream ENSMUSE00000640047 Chr2:152052621..152052727 CCGCCATATTGTCTGTGTGA Chr2:152052665..152052684 60.54 50
upstream ENSMUSE00000640046 Chr2:152076138..152076347 CCAACGTCTGCTTTTGAACA Chr2:152076170..152076189 59.88 45
upstream ENSMUSE00000640045 Chr2:152079946..152080057 TTGAAGCCATCAACATCACAA Chr2:152080005..152080025 60.1 38.1
upstream ENSMUSE00000640044 Chr2:152083114..152083215 CCCAACATCATCACACTTGC Chr2:152083174..152083193 59.97 50
upstream ENSMUSE00000640043 Chr2:152083677..152083727 CCTGCCTTGGTTTTTGAACA Chr2:152083686..152083705 61.03 45
upstream ENSMUSE00000640042 Chr2:152084412..152084471 No primer for this exon
upstream ENSMUSE00000711309 Chr2:152086495..152086578 ACAGCATGGGGATTATGCAC Chr2:152086511..152086530 60.75 50
upstream ENSMUSE00000712610 Chr2:152086495..152086578 ACAGCATGGGGATTATGCAC Chr2:152086511..152086530 60.75 50
upstream ENSMUSE00000640040 Chr2:152088919..152089029 TTTACCATCCAGGCCAAGAG Chr2:152088950..152088969 60.07 50
upstream ENSMUSE00000681807 Chr2:152088919..152089029 TTTACCATCCAGGCCAAGAG Chr2:152088950..152088969 60.07 50

*** Putative Vector Insertion (Chr 2: 152089030 - 152098363) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000640038 Chr2:152098364..152098465 ACCCAAGCTCCACATATCCA Chr2:152098402..152098421 60.34 50
downstream ENSMUSE00000681805 Chr2:152098364..152098465 ACCCAAGCTCCACATATCCA Chr2:152098402..152098421 60.34 50
downstream ENSMUSE00000640037 Chr2:152099829..152099929 AACCTTGGCTATCCTCACCA Chr2:152099852..152099871 59.55 50
downstream ENSMUSE00000681804 Chr2:152099829..152099929 AACCTTGGCTATCCTCACCA Chr2:152099852..152099871 59.55 50
downstream ENSMUSE00000640036 Chr2:152101134..152101282 TCACTGTGGACAAAGCGTTC Chr2:152101175..152101194 59.88 50
downstream ENSMUSE00000681802 Chr2:152101134..152101282 TCACTGTGGACAAAGCGTTC Chr2:152101175..152101194 59.88 50
downstream ENSMUSE00000640035 Chr2:152102683..152102769 GCCTGGTCCTTCACAACAGT Chr2:152102707..152102726 60.16 55
downstream ENSMUSE00000681801 Chr2:152102683..152102769 GCCTGGTCCTTCACAACAGT Chr2:152102707..152102726 60.16 55
downstream ENSMUSE00000539955 Chr2:152104705..152107581 AGTTATCCACAGCGGTCCAC Chr2:152107079..152107098 60 55
downstream ENSMUSE00000681799 Chr2:152104705..152106074 AAATCCACAAGCAACGGTTC Chr2:152104955..152104974 59.98 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CATTAATCGCCTTGCAGCAC Chr2:152095078..152095098 61.69 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGAACGTGACTGGGAAAACC Chr2:152092077..152092097 60.93 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000074698