Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29142
Trapped Gene
Usp9x (ENSMUSG00000031010)
Vector Insertion
Chr X: 12736071 - 12736899
Public Clones not available
Private Clones OST7398 (lexicon)
Severity of mutation (?) Insertion after 84% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000624757 (ChrX:12735845..12736070 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTTGCATCTCCTGGACCTTC ChrX:12736044..12736063 60.19 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000624757 (ChrX:12735845..12736070 +)
Downstram Exon
ENSMUSE00000624756 (ChrX:12736900..12737029 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTTGCATCTCCTGGACCTTC ChrX:12736044..12736063 60.19 50 CTCCCTCCGCAAGAGATTTA ChrX:12736968..12736987 59.41 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000702979 ChrX:12648624..12648859 TTTGTTGGGTTCGCCATATT ChrX:12648774..12648793 60.19 40
upstream ENSMUSE00000707355 ChrX:12648640..12648859 TTTGTTGGGTTCGCCATATT ChrX:12648774..12648793 60.19 40
upstream ENSMUSE00000372304 ChrX:12648663..12648848 TTTGTTGGGTTCGCCATATT ChrX:12648774..12648793 60.19 40
upstream ENSMUSE00000407874 ChrX:12671042..12671303 TCGAGTATGACAGCCACGAC ChrX:12671202..12671221 59.86 55
upstream ENSMUSE00000702978 ChrX:12671050..12671303 TCGAGTATGACAGCCACGAC ChrX:12671202..12671221 59.86 55
upstream ENSMUSE00000720743 ChrX:12671050..12671303 TCGAGTATGACAGCCACGAC ChrX:12671202..12671221 59.86 55
upstream ENSMUSE00000205428 ChrX:12675576..12675721 AGGAACCTGCATTTCCACAC ChrX:12675667..12675686 59.97 50
upstream ENSMUSE00000205393 ChrX:12677559..12677638 CTCGATGGGTTGTTCCAGTT ChrX:12677561..12677580 59.97 50
upstream ENSMUSE00000205407 ChrX:12680454..12680566 TGAAGCATGTCAGCGATTTT ChrX:12680470..12680489 59.42 40
upstream ENSMUSE00000205423 ChrX:12681709..12681927 CTGCGAGTCAGTGTCCTCAA ChrX:12681849..12681868 60.18 55
upstream ENSMUSE00000205400 ChrX:12684191..12684306 CTCCTCAACAAGTTTGGCACT ChrX:12684206..12684226 59.39 47.62
upstream ENSMUSE00000205394 ChrX:12684790..12685041 GAATTTAGCTTCGCGGGTTC ChrX:12684964..12684983 61.06 50
upstream ENSMUSE00000205395 ChrX:12685116..12685254 CATGGCAGTTCTGAGGATGA ChrX:12685207..12685226 59.79 50
upstream ENSMUSE00000205434 ChrX:12687202..12687354 CGAGATAGCCTTCATCAACCA ChrX:12687241..12687261 60.22 47.62
upstream ENSMUSE00000482455 ChrX:12688218..12688322 AGGGAAACATGAAGCCATTG ChrX:12688220..12688239 59.93 45
upstream ENSMUSE00000205425 ChrX:12690686..12690892 TGAGCTGATTCGTCGTCTTG ChrX:12690730..12690749 60.14 50
upstream ENSMUSE00000205438 ChrX:12691634..12691770 AAATGGGTCATTCCTGCACT ChrX:12691697..12691716 59.41 45
upstream ENSMUSE00000205398 ChrX:12693750..12693883 TCAGCGAAGTCCCCATGTAT ChrX:12693756..12693775 60.48 50
upstream ENSMUSE00000205401 ChrX:12698559..12698646 CACAAACTGTGAGACTGGGAAG ChrX:12698577..12698598 59.8 50
upstream ENSMUSE00000703046 ChrX:12700294..12700636 TGCTTCAGCTTGATCCTTCC ChrX:12700479..12700498 60.48 50
upstream ENSMUSE00000624777 ChrX:12701694..12701789 TGCCGAGCTATTGATCTCCT ChrX:12701724..12701743 59.94 50
upstream ENSMUSE00000624776 ChrX:12702522..12702733 GTTCGAATGGTCCGAGTGTT ChrX:12702639..12702658 59.97 50
upstream ENSMUSE00000624775 ChrX:12705334..12705574 TCCTGGAGATGACCGAAAGT ChrX:12705523..12705542 59.65 50
upstream ENSMUSE00000624774 ChrX:12706103..12706252 GGAAAGTTGTTTGCCTGGAG ChrX:12706231..12706250 59.71 50
upstream ENSMUSE00000624773 ChrX:12707352..12707472 GCAGCCTAAATATGCCACCT ChrX:12707410..12707429 59.21 50
upstream ENSMUSE00000624772 ChrX:12708853..12708983 GTTTGGACCATGCCAAACTT ChrX:12708886..12708905 59.84 45
upstream ENSMUSE00000624771 ChrX:12709196..12709474 GAAGGGGTGCCTACCTCAAT ChrX:12709347..12709366 60.33 55
upstream ENSMUSE00000624770 ChrX:12712070..12712195 GCAGTGGTGCTACAAAGTGC ChrX:12712094..12712113 59.52 55
upstream ENSMUSE00000624769 ChrX:12713571..12713696 TGGTATTCAGCCCAAATGAA ChrX:12713653..12713672 58.97 40
upstream ENSMUSE00000624768 ChrX:12714734..12714900 AATGAGCCAGACCTCGAAGA ChrX:12714746..12714765 59.95 50
upstream ENSMUSE00000624767 ChrX:12717235..12717343 ACTGTTCGTCAAGTGGCACA ChrX:12717236..12717255 60.36 50
upstream ENSMUSE00000624766 ChrX:12717536..12717682 TTAATGTGCCCAATGCTGAA ChrX:12717621..12717640 60.07 40
upstream ENSMUSE00000624765 ChrX:12718833..12718979 AGGACACCTTGGGGTTACAA ChrX:12718883..12718902 59.3 50
upstream ENSMUSE00000624764 ChrX:12721412..12721634 GACTTCATCTTTCCCGCATC ChrX:12721424..12721443 59.63 50
upstream ENSMUSE00000624763 ChrX:12722253..12722473 CGTCCACCAAAAGGATTTGT ChrX:12722300..12722319 59.83 45
upstream ENSMUSE00000624762 ChrX:12725071..12725261 TTTGGCCATTTAGCTGCTTC ChrX:12725197..12725216 60.34 45
upstream ENSMUSE00000624761 ChrX:12728396..12728569 GGGCATCCAGCTATGCTAAG ChrX:12728493..12728512 59.83 55
upstream ENSMUSE00000624760 ChrX:12731218..12731359 No primer for this exon
upstream ENSMUSE00000624759 ChrX:12733120..12733873 ATCCGCCATTGAAAGAAGTG ChrX:12733740..12733759 60.07 45
upstream ENSMUSE00000624758 ChrX:12734795..12734918 TAGTCCGAGGATCTGCCAGT ChrX:12734894..12734913 59.83 55
upstream ENSMUSE00000624757 ChrX:12735845..12736070 TTTGCATCTCCTGGACCTTC ChrX:12736044..12736063 60.19 50

*** Putative Vector Insertion (Chr X: 12736071 - 12736899) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000624756 ChrX:12736900..12737029 CTCCCTCCGCAAGAGATTTA ChrX:12736968..12736987 59.41 50
downstream ENSMUSE00000624755 ChrX:12737873..12738058 ATTTAATTGGAGGGCCAGGA ChrX:12737968..12737987 60.63 45
downstream ENSMUSE00000624754 ChrX:12738440..12738660 GCAATTTGACGGTCTCATCA ChrX:12738598..12738617 59.65 45
downstream ENSMUSE00000624753 ChrX:12738749..12738837 AAATAGGGCCGGAGTTCATAA ChrX:12738788..12738808 59.82 42.86
downstream ENSMUSE00000624752 ChrX:12741838..12741994 TTGTGTCAAACAGCCCATCT ChrX:12741896..12741915 59.14 45
downstream ENSMUSE00000624751 ChrX:12742398..12742610 CATCTCCAAGCCACTCCACT ChrX:12742455..12742474 60.26 55
downstream ENSMUSE00000624750 ChrX:12743758..12743853 TTGAGATCCAGGGGAATGAG ChrX:12743847..12743866 60 50
downstream ENSMUSE00000501079 ChrX:12746473..12746598 GACACTTCTTCACCGCCTTC ChrX:12746588..12746607 59.85 55
downstream ENSMUSE00000519250 ChrX:12746473..12750454 ACTAGGCTCCAGCCAGCATA ChrX:12747564..12747583 60 55
downstream ENSMUSE00000702977 ChrX:12746601..12750454 ACTAGGCTCCAGCCAGCATA ChrX:12747564..12747583 60 55
downstream ENSMUSE00000702981 ChrX:12766664..12766815 GACACTTCTTCACCGCCTTC ChrX:12766779..12766798 59.85 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTTGTCCTTCACCTTTTGC ChrX:12736030..12736050 59.71 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTTGTCCTTCACCTTTTGC ChrX:12736030..12736050 59.71 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000031010