Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31953
Trapped Gene
Rims2 (ENSMUSG00000037386)
Vector Insertion
Chr 15: 39448057 - 39491330
Public Clones IST12558E7 (tigm) IST10169F9 (tigm) IST12259A11 (tigm) IST12687C11 (tigm)
IST12687C11 (tigm) IST12337E11 (tigm) IST12687D11 (tigm) IST11278C10 (tigm)
IST10710D1 (tigm) IST12259A11 (tigm) IST10169F10 (tigm) IST12337E11 (tigm)
IST12733F11 (tigm) IST10710D1 (tigm) IST12723H1 (tigm) IST10850D12 (tigm)
IST10111H8 (tigm) IST10850D12 (tigm) IST10169F9 (tigm) IST13083H7 (tigm)
IST10038C8 (tigm) IST13083H7 (tigm) IST10074B6 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000562061 (Chr15:39447815..39448056 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAAAGTCGCAGTGCCTCTC Chr15:39448022..39448041 60.14 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000562061 (Chr15:39447815..39448056 +)
Downstram Exon
ENSMUSE00000683479 (Chr15:39491331..39491472 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAAAGTCGCAGTGCCTCTC Chr15:39448022..39448041 60.14 55 GCCAGCTAGAGCCTCAAAAG Chr15:39491435..39491454 59.36 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000508133 Chr15:39029878..39030084 GCTGTCATGGATCGTCAGAA Chr15:39030032..39030051 59.79 50
upstream ENSMUSE00000562094 Chr15:39106522..39106554 ACACAAAGCACAACCGACAC Chr15:39106534..39106553 59.65 50
upstream ENSMUSE00000562092 Chr15:39106960..39107046 AATGAGAAGGAGCCCCAGAC Chr15:39107027..39107046 60.6 55
upstream ENSMUSE00000474739 Chr15:39123648..39123858 TTGCCAAACCAAGTTCTGTG Chr15:39123801..39123820 59.73 45
upstream ENSMUSE00000473739 Chr15:39176856..39177166 TGCAGCAACCTGATCAAAAG Chr15:39176944..39176963 59.99 45
upstream ENSMUSE00000683481 Chr15:39223668..39223789 ACAAACGCTGAACAATGCAA Chr15:39223769..39223788 60.3 40
upstream ENSMUSE00000460906 Chr15:39268543..39269468 TGAACGTAGAGCTGCAATGG Chr15:39269038..39269057 60.01 50
upstream ENSMUSE00000562027 Chr15:39283586..39283653 AAGCGTCTTGGCATAGCAGT Chr15:39283613..39283632 60.04 50
upstream ENSMUSE00000562090 Chr15:39283770..39283978 ACAACCCTTAACGAGGAGCA Chr15:39283943..39283962 59.73 50
upstream ENSMUSE00000562089 Chr15:39285906..39286025 ACCTCGAGACTCAGGAGCAA Chr15:39285992..39286011 60.13 55
upstream ENSMUSE00000562088 Chr15:39288224..39288323 CAGGTCGACTTTGTGCATTT Chr15:39288249..39288268 58.78 45
upstream ENSMUSE00000562086 Chr15:39289310..39289433 AGGAGCCACATTTGAGGAAG Chr15:39289347..39289366 59.28 50
upstream ENSMUSE00000562084 Chr15:39291135..39291181 GATAGCACGCATGCACAACT Chr15:39291154..39291173 59.9 50
upstream ENSMUSE00000562083 Chr15:39294044..39294156 CCCGCAGTTCTTATCTGGAC Chr15:39294129..39294148 59.69 55
upstream ENSMUSE00000562080 Chr15:39303880..39304010 TGACAAGGTTGGTCACCAGT Chr15:39303894..39303913 58.99 50
upstream ENSMUSE00000562078 Chr15:39307926..39308097 GAATTCCGTGAACGAATGCT Chr15:39308017..39308036 60.08 45
upstream ENSMUSE00000562076 Chr15:39310103..39310256 GCAGACCCATGATGTCTCCT Chr15:39310159..39310178 60.08 55
upstream ENSMUSE00000562075 Chr15:39338512..39338580 TGACTACGACTGCGAGGATG Chr15:39338543..39338562 60.01 55
upstream ENSMUSE00000562072 Chr15:39341191..39341347 AAGGTCATGGTCGCCTAGTG Chr15:39341312..39341331 60.13 55
upstream ENSMUSE00000562070 Chr15:39342810..39342920 No primer for this exon
upstream ENSMUSE00000562026 Chr15:39366384..39366563 CCTTCACCTGCCTTATCGAG Chr15:39366544..39366563 59.83 55
upstream ENSMUSE00000562069 Chr15:39367418..39367527 CAAGTACTCCGGGAACAGGA Chr15:39367456..39367475 60.1 55
upstream ENSMUSE00000562045 Chr15:39398489..39398589 GGAGAGAAATCGCCAAATGA Chr15:39398505..39398524 60.15 45
upstream ENSMUSE00000562064 Chr15:39417136..39417308 CAAGCTACATGTCCGTCCAA Chr15:39417257..39417276 59.72 50
upstream ENSMUSE00000562023 Chr15:39441610..39441687 GGAGCACAGACACCAGTTCA Chr15:39441635..39441654 59.87 55
upstream ENSMUSE00000562061 Chr15:39447815..39448056 GAAAAGTCGCAGTGCCTCTC Chr15:39448022..39448041 60.14 55

*** Putative Vector Insertion (Chr 15: 39448057 - 39491330) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000683479 Chr15:39491331..39491472 GCCAGCTAGAGCCTCAAAAG Chr15:39491435..39491454 59.36 55
downstream ENSMUSE00000229123 Chr15:39506486..39506627 TAGCTGTTCATGCTGCCATC Chr15:39506615..39506634 59.98 50
downstream ENSMUSE00000229120 Chr15:39510794..39510906 AGGCCATCCAGGAAATCACT Chr15:39510859..39510878 60.85 50
downstream ENSMUSE00000229114 Chr15:39511176..39511277 CCGGATGATTTCTACCTCCA Chr15:39511237..39511256 59.89 50
downstream ENSMUSE00000229108 Chr15:39512535..39512674 GGCTATGCAGACTCCGTTGT Chr15:39512584..39512603 60.28 55
downstream ENSMUSE00000562051 Chr15:39513092..39513486 CAGAGACGATTGGGAAGCTC Chr15:39513277..39513296 59.95 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTACTGCTGCCCCCTAACAT Chr15:39478074..39478094 59.59 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTTACTGCTGCCCCCTAAC Chr15:39478072..39478092 59.22 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037386