Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29035
Trapped Gene
Ckap5 (ENSMUSG00000040549)
Vector Insertion
Chr 2: 91386573 - 91388930
Public Clones not available
Private Clones OST11631 (lexicon)
Severity of mutation (?) Insertion after 1% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000643314 (Chr2:91386479..91386572 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGGAGATGACAGTGAGTGG Chr2:91386517..91386536 59.66 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000643314 (Chr2:91386479..91386572 +)
Downstram Exon
ENSMUSE00000167374 (Chr2:91388931..91389124 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGGAGATGACAGTGAGTGG Chr2:91386517..91386536 59.66 55 TTTCCTGCAACATGAGCATT Chr2:91389127..91389146 59.28 40

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000643315 Chr2:91366994..91367007 No primer for this exon
upstream ENSMUSE00000643314 Chr2:91386479..91386572 TGGGAGATGACAGTGAGTGG Chr2:91386517..91386536 59.66 55
upstream ENSMUSE00000399736 Chr2:91386490..91386572 TGGGAGATGACAGTGAGTGG Chr2:91386517..91386536 59.66 55

*** Putative Vector Insertion (Chr 2: 91386573 - 91388930) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000167374 Chr2:91388931..91389124 TTTCCTGCAACATGAGCATT Chr2:91389127..91389146 59.28 40
downstream ENSMUSE00000390637 Chr2:91390709..91390915 TTGTTATCCAGGCCCTTCAG Chr2:91390867..91390886 60.07 50
downstream ENSMUSE00000352788 Chr2:91395424..91395595 TTCACAGCATCTCGATTCCA Chr2:91395567..91395586 60.35 45
downstream ENSMUSE00000167375 Chr2:91396657..91396789 CAGAAACCGACTGGGCTTAG Chr2:91396725..91396744 59.87 55
downstream ENSMUSE00000167380 Chr2:91397732..91397832 GGATCTCTACCGCATCCAGA Chr2:91397800..91397819 60.18 55
downstream ENSMUSE00000371865 Chr2:91399206..91399319 No primer for this exon
downstream ENSMUSE00000519590 Chr2:91400964..91401068 CCAACATGACATTGGTGTCC Chr2:91400997..91401016 59.66 50
downstream ENSMUSE00000687485 Chr2:91402911..91403000 GATTGCATCAATTGCCTCCT Chr2:91402994..91403013 60.04 45
downstream ENSMUSE00000167373 Chr2:91403106..91403270 CTGCTTGATGGTGGGATTTT Chr2:91403177..91403196 59.93 45
downstream ENSMUSE00000167378 Chr2:91404477..91404605 CCACCTTCAAAGCTGTACCC Chr2:91404549..91404568 59.59 55
downstream ENSMUSE00000167392 Chr2:91405778..91405960 TTTTAACGGTCCTGGTTTGG Chr2:91405945..91405964 59.83 45
downstream ENSMUSE00000167369 Chr2:91408294..91408407 TATTCTTTGTCCCGGCACTT Chr2:91408366..91408385 59.57 45
downstream ENSMUSE00000167382 Chr2:91408794..91408904 TGAATACAGGTTGGGGGAAG Chr2:91408849..91408868 59.78 50
downstream ENSMUSE00000167390 Chr2:91410337..91410429 GCATCTCAGTTCGCTCCATT Chr2:91410370..91410389 60.37 50
downstream ENSMUSE00000167371 Chr2:91412505..91412690 TCTTTTGCATTGTTCCCACA Chr2:91412641..91412660 60.09 40
downstream ENSMUSE00000449769 Chr2:91413130..91413224 TTTTGTGAGAAGGCCATTGA Chr2:91413158..91413177 59.25 40
downstream ENSMUSE00000449762 Chr2:91416173..91416230 TGTTGCAGCAAGAGCAGTCT Chr2:91416227..91416246 59.93 50
downstream ENSMUSE00000449758 Chr2:91416320..91416445 TGATGGCAGAAGTCCTCACA Chr2:91416344..91416363 60.4 50
downstream ENSMUSE00000449749 Chr2:91417721..91417860 GATCTCAATCCTCGGCAAAA Chr2:91417861..91417880 60.15 45
downstream ENSMUSE00000449746 Chr2:91418192..91418366 TCAAGGCAGTTGGAAGTTCA Chr2:91418337..91418356 59.42 45
downstream ENSMUSE00000449741 Chr2:91419580..91419693 GGATGCCCAGGTTCTTTACA Chr2:91419667..91419686 59.93 50
downstream ENSMUSE00000449733 Chr2:91421267..91421395 TTCATGCCAGTTTGTTCTGC Chr2:91421331..91421350 59.85 45
downstream ENSMUSE00000449729 Chr2:91425879..91426073 GGGCCTTCTTCCGTACATCT Chr2:91426005..91426024 60.46 55
downstream ENSMUSE00000449724 Chr2:91426395..91426530 TTTGGCCTTTTCTAGCATGG Chr2:91426442..91426461 60.2 45
downstream ENSMUSE00000449280 Chr2:91428826..91428914 AAGAAACGCCTGGAGCTTTA Chr2:91428906..91428925 59.11 45
downstream ENSMUSE00000449277 Chr2:91431823..91431948 TTTGCTTGGCACTTTCTTCC Chr2:91431855..91431874 60.37 45
downstream ENSMUSE00000385033 Chr2:91434840..91434989 TCATCCCGTGGGGTAGTAAA Chr2:91434877..91434896 60.18 50
downstream ENSMUSE00000301737 Chr2:91435468..91435671 AGGGGATAAAGGACGATGCT Chr2:91435660..91435679 59.92 50
downstream ENSMUSE00000301727 Chr2:91435845..91435980 CACATCCGGTTCAGGATAGC Chr2:91435906..91435925 60.48 55
downstream ENSMUSE00000301721 Chr2:91436519..91436712 TTCCGTACAGCATTGTCTCG Chr2:91436645..91436664 59.86 50
downstream ENSMUSE00000301714 Chr2:91439363..91439535 TGCTGACCGCTTTATCCTCT Chr2:91439416..91439435 59.98 50
downstream ENSMUSE00000301705 Chr2:91440798..91440971 TTTCACAGCGGACTGTACCA Chr2:91440910..91440929 60.3 50
downstream ENSMUSE00000301700 Chr2:91441163..91441283 TCAGAGCTTGGATGCTTGTG Chr2:91441281..91441300 60.14 50
downstream ENSMUSE00000301692 Chr2:91446403..91446582 TGATCAATGTGGCCAGACAT Chr2:91446464..91446483 59.92 45
downstream ENSMUSE00000391433 Chr2:91447602..91447789 TCACCACCAAGAGGTTCACA Chr2:91447755..91447774 60.13 50
downstream ENSMUSE00000301675 Chr2:91452897..91452972 AGCTGTTGCTAGCAGGCTGT Chr2:91452942..91452961 60.36 55
downstream ENSMUSE00000362729 Chr2:91455130..91455318 TGCTGTTGATGGTGTCAGGT Chr2:91455178..91455197 60.16 50
downstream ENSMUSE00000301668 Chr2:91455399..91455536 ATGCTTCATCATCCGACACA Chr2:91455479..91455498 60.08 45
downstream ENSMUSE00000301660 Chr2:91455951..91456034 TGGCCTTTGATGATTTTTCA Chr2:91455975..91455994 59.09 35
downstream ENSMUSE00000380899 Chr2:91456458..91456617 GCCTTTGCTTTCTCTCTCCA Chr2:91456601..91456620 59.69 50
downstream ENSMUSE00000687475 Chr2:91459845..91459996 GCACACATGTGACCTCCATC Chr2:91459880..91459899 59.97 55
downstream ENSMUSE00000336116 Chr2:91459908..91459996 GTAGACAGATGGCCCCACTT Chr2:91459948..91459967 59.02 55
downstream ENSMUSE00000373938 Chr2:91460139..91460819 CAACTGGAGGAATTGCTGGT Chr2:91460199..91460218 60.11 50
downstream ENSMUSE00000687474 Chr2:91460139..91460820 CAACTGGAGGAATTGCTGGT Chr2:91460199..91460218 60.11 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGATCAGAAATGTGAACACAAGG Chr2:91386552..91386575 60.02 39.13 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGATCAGAAATGTGAACACAAGG Chr2:91386552..91386575 60.02 39.13 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040549