Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1820
Trapped Gene
Fbxl10 (ENSMUSG00000029475)
Vector Insertion
Chr 5: 123350360 - 123371393
Public Clones AL0304 (sanger) AB0140 (sanger) CA0031 (sanger) RRT430 (baygenomics)
XL516 (baygenomics) RRT156 (baygenomics) CMHD-GT_525B4-5S (cmhd) IST12188F10HMR1 (tigm)
IST12187D12HMR1 (tigm) IST14182B5 (tigm) IST11041E8 (tigm) IST12184E1HMR1 (tigm)
IST12172H12BBR1 (tigm) IST11792B7 (tigm) IST15060E8 (tigm) IST12188H9HMR1 (tigm)
IST14548B11 (tigm) IST11550D5 (tigm) IST10917G2 (tigm) IST12191G7HMR1 (tigm)
IST12187D12BBR1 (tigm) IST12830A10 (tigm) IST14455H7 (tigm) IST12184B6HMR1 (tigm)
IST10755F7 (tigm) IST10944G11 (tigm) IST10881D6 (tigm) IST12188F10BBR1 (tigm)
IST10917D7 (tigm) IST15012D3 (tigm) IST10837C12 (tigm) IST12179C8HMR1 (tigm)
IST12172H12HMR1 (tigm) IST14394H12 (tigm) IST14535A7 (tigm) IST12173H8HMR1 (tigm)
IST14423B10 (tigm) IST14418E11 (tigm) IST14992E7 (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
ENSMUSE00000382139 (Chr5:123371394..123371480 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGAAAGAGCACGTGGATGA Chr5:123371455..123371474 59.98 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000382139 (Chr5:123371394..123371480 -)
Downstram Exon
ENSMUSE00000537526 (Chr5:123350158..123350359 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGAAAGAGCACGTGGATGA Chr5:123371455..123371474 59.98 50 GGCTCCGATTCATAGTCGTC Chr5:123350143..123350162 59.66 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000717210 Chr5:123439634..123439832 CGCAAATGGATAAGGGTCTG Chr5:123439731..123439750 60.46 50
upstream ENSMUSE00000518745 Chr5:123438877..123438909 No primer for this exon
upstream ENSMUSE00000714097 Chr5:123438877..123439315 TTACGTTCCGGGGATTATGA Chr5:123439130..123439149 60.15 45
upstream ENSMUSE00000593008 Chr5:123438476..123438542 GGGGAGTCTCCTTAGGAAGTG Chr5:123438516..123438536 59.19 57.14
upstream ENSMUSE00000338385 Chr5:123437671..123437815 TATACCAGGGGGACTTCGTG Chr5:123437690..123437709 59.81 55
upstream ENSMUSE00000376150 Chr5:123434471..123434549 TTCGGGACAAGGATGGACTA Chr5:123434479..123434498 60.45 50
upstream ENSMUSE00000328593 Chr5:123432786..123432832 TGATTTCACAGTCCGAGACG Chr5:123432801..123432820 59.83 50
upstream ENSMUSE00000328661 Chr5:123411419..123411597 CCAGAAGGGTACCGAGATGA Chr5:123411541..123411560 60.06 55
upstream ENSMUSE00000328656 Chr5:123411022..123411128 GTGGCCTCAGCATCTAAAGG Chr5:123411080..123411099 59.84 55
upstream ENSMUSE00000328651 Chr5:123399079..123399172 ACCTCCGTGTGGTACCATGT Chr5:123399095..123399114 60.16 55
upstream ENSMUSE00000328643 Chr5:123397736..123397889 GTACGAGGAGTGGGTGCTGT Chr5:123397829..123397848 60.18 60
upstream ENSMUSE00000328635 Chr5:123390962..123391077 GGATCCATGCGGTTTATACG Chr5:123391055..123391074 60.17 50
upstream ENSMUSE00000328629 Chr5:123384742..123384868 GTTCAGCCCAAGTTCCGTTA Chr5:123384849..123384868 60.11 50
upstream ENSMUSE00000331402 Chr5:123382476..123382960 AGGACAAGGAGGAGGAAGGA Chr5:123382836..123382855 60.19 55
upstream ENSMUSE00000382139 Chr5:123371394..123371480 CTGAAAGAGCACGTGGATGA Chr5:123371455..123371474 59.98 50

*** Putative Vector Insertion (Chr 5: 123350360 - 123371393) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000537526 Chr5:123350158..123350359 GGCTCCGATTCATAGTCGTC Chr5:123350143..123350162 59.66 55
downstream ENSMUSE00000328745 Chr5:123338539..123338763 AGTGGCACTCTCCACACTCC Chr5:123338591..123338610 60.31 60
downstream ENSMUSE00000437855 Chr5:123333328..123333471 GTGGATGATCTCGTTGCAGA Chr5:123333321..123333340 59.79 50
downstream ENSMUSE00000247403 Chr5:123332411..123332497 GAAGCTCATCGTTGACCACA Chr5:123332439..123332458 59.84 50
downstream ENSMUSE00000437831 Chr5:123331973..123332233 CTTGTTGTCCCGGTTCATCT Chr5:123332128..123332147 59.97 50
downstream ENSMUSE00000437825 Chr5:123331646..123331759 GGCTGAGACTGCTGCCTAGA Chr5:123331662..123331681 60.84 60
downstream ENSMUSE00000437822 Chr5:123331029..123331067 No primer for this exon
downstream ENSMUSE00000412900 Chr5:123330182..123330861 GTGAGCTGGAACGTGACTGA Chr5:123330701..123330720 60.03 55
downstream ENSMUSE00000189235 Chr5:123329498..123329661 CCAACTGAGGTCAAGGGAGA Chr5:123329525..123329544 60.23 55
downstream ENSMUSE00000189228 Chr5:123329254..123329415 CCTCATCTGGGCATCCTTTA Chr5:123329266..123329285 60.03 50
downstream ENSMUSE00000189233 Chr5:123328444..123328662 AGGCGCAGCTCTACAATGTT Chr5:123328592..123328611 60.04 50
downstream ENSMUSE00000716214 Chr5:123321714..123321906 AGCGTTTGAAGAAGGACAGG Chr5:123321840..123321859 59.47 50
downstream ENSMUSE00000593009 Chr5:123320690..123321906 TGCATCAGGGAAAGGTTAGG Chr5:123320702..123320721 60.07 50
downstream ENSMUSE00000719227 Chr5:123320688..123321906 TGCATCAGGGAAAGGTTAGG Chr5:123320702..123320721 60.07 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAGCCTCCCCAACCATACCT Chr5:123362350..123362370 60.7 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAGCCTCCCCAACCATACCT Chr5:123362350..123362370 60.7 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CATTGGTGCTTGTTTTCAGG Chr5:123371433..123371453 59.17 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CATTGGTGCTTGTTTTCAGG Chr5:123371433..123371453 59.17 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029475