Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1593
Trapped Gene
Ncor2 (ENSMUSG00000029478)
Vector Insertion
Chr 5: 125516497 - 125517190
Public Clones CC0027 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 49% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000389863 (Chr5:125517191..125517288 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000389863 (Chr5:125517191..125517288 -)
Downstram Exon
ENSMUSE00000318514 (Chr5:125516346..125516496 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon ATAGGACGTGGCCTTTCTTG Chr5:125516333..125516352 59.19 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000536603 Chr5:125659367..125659423 No primer for this exon
upstream ENSMUSE00000687687 Chr5:125659367..125659550 No primer for this exon
upstream ENSMUSE00000687689 Chr5:125659367..125659572 No primer for this exon
upstream ENSMUSE00000687704 Chr5:125659367..125659589 No primer for this exon
upstream ENSMUSE00000687761 Chr5:125659367..125659584 No primer for this exon
upstream ENSMUSE00000687760 Chr5:125633977..125634022 TTTGAGGAACACAGCCTCCT Chr5:125633991..125634010 59.84 50
upstream ENSMUSE00000318715 Chr5:125605140..125605270 CTACCTGGACCCTACCACCA Chr5:125605244..125605263 59.84 60
upstream ENSMUSE00000471726 Chr5:125605140..125605350 CTACCTGGACCCTACCACCA Chr5:125605244..125605263 59.84 60
upstream ENSMUSE00000719098 Chr5:125605140..125605350 CTACCTGGACCCTACCACCA Chr5:125605244..125605263 59.84 60
upstream ENSMUSE00000318709 Chr5:125599852..125599979 ATCATCCAGCCACAGAGGAG Chr5:125599894..125599913 60.22 55
upstream ENSMUSE00000687686 Chr5:125599852..125599979 ATCATCCAGCCACAGAGGAG Chr5:125599894..125599913 60.22 55
upstream ENSMUSE00000318701 Chr5:125598987..125599164 AGAATTCACCGAGAGCAAGC Chr5:125599079..125599098 59.58 50
upstream ENSMUSE00000687685 Chr5:125598987..125599164 AGAATTCACCGAGAGCAAGC Chr5:125599079..125599098 59.58 50
upstream ENSMUSE00000318694 Chr5:125590263..125590442 CTCGACTGTCCAAGGAGGAG Chr5:125590341..125590360 59.98 60
upstream ENSMUSE00000517037 Chr5:125586569..125586682 CCACCCATAGAATCAAAGCA Chr5:125586606..125586625 58.57 45
upstream ENSMUSE00000318682 Chr5:125583013..125583069 No primer for this exon
upstream ENSMUSE00000189256 Chr5:125578317..125578369 TACAACCAGCCGTCTGACAC Chr5:125578344..125578363 59.75 55
upstream ENSMUSE00000189280 Chr5:125572024..125572090 GATGCGGAAGAAGCTGATCT Chr5:125572062..125572081 59.54 50
upstream ENSMUSE00000189271 Chr5:125568164..125568336 TAGAGAACAATCCGCGAAGG Chr5:125568253..125568272 60.34 50
upstream ENSMUSE00000189250 Chr5:125567211..125567304 ATGGCTTGTCTGAGCAGGAG Chr5:125567211..125567230 60.56 55
upstream ENSMUSE00000318654 Chr5:125565251..125565429 GGTCTACAAGGACCGTCAGG Chr5:125565297..125565316 59.57 60
upstream ENSMUSE00000189246 Chr5:125561500..125561554 CCCTAAGAACTTTGGCCTGA Chr5:125561523..125561542 59.31 50
upstream ENSMUSE00000189289 Chr5:125559378..125559476 GGTCGCTGAGTGTGTCCTCT Chr5:125559455..125559474 60.47 60
upstream ENSMUSE00000318635 Chr5:125549302..125549447 CGGAGAACGAGAAGGAAGAA Chr5:125549310..125549329 59.54 50
upstream ENSMUSE00000189296 Chr5:125548146..125548318 ACACTTCTGGCGAGGACAAC Chr5:125548285..125548304 60.31 55
upstream ENSMUSE00000189292 Chr5:125546210..125546272 AGTTCTCGCTGGACTGAGGA Chr5:125546233..125546252 60.13 55
upstream ENSMUSE00000189258 Chr5:125536103..125536245 CAAGACCGTGTCCCAGTGTA Chr5:125536174..125536193 59.59 55
upstream ENSMUSE00000189275 Chr5:125531281..125531428 AGGACGAAGAGATGGAAGCA Chr5:125531327..125531346 59.95 50
upstream ENSMUSE00000189249 Chr5:125529712..125529765 GGGAATGAGGTTCCCAGAGT Chr5:125529732..125529751 60.31 55
upstream ENSMUSE00000189272 Chr5:125528702..125528904 TCCAGAAGAACCGGCAGTAG Chr5:125528758..125528777 60.39 55
upstream ENSMUSE00000189253 Chr5:125528575..125528697 CGGCTACTGTGGACAAGGAT Chr5:125528660..125528679 60.13 55
upstream ENSMUSE00000189247 Chr5:125528310..125528572 ACCCAGGACAGTGACTCCAG Chr5:125528364..125528383 60.15 60
upstream ENSMUSE00000536639 Chr5:125528310..125528904 GAGGAGATCGATGTGGGAAA Chr5:125528574..125528593 60.01 50
upstream ENSMUSE00000318572 Chr5:125523115..125523235 CTGGACCTGAAGCAGCTGAA Chr5:125523143..125523162 61.67 55
upstream ENSMUSE00000189293 Chr5:125522166..125522334 GAGGACACAGTACCCCCAAA Chr5:125522288..125522307 59.82 55
upstream ENSMUSE00000687688 Chr5:125522166..125522337 GAGGACACAGTACCCCCAAA Chr5:125522288..125522307 59.82 55
upstream ENSMUSE00000331878 Chr5:125519259..125519423 GATCAAGACTTCCCCACACG Chr5:125519295..125519314 60.51 55
upstream ENSMUSE00000318541 Chr5:125518231..125518367 CATCTCCTCTGCCAAGCATC Chr5:125518269..125518288 60.91 55
upstream ENSMUSE00000392132 Chr5:125517644..125517749 GGATGTCAGTCCAGCTTCGT Chr5:125517726..125517745 60.27 55
upstream ENSMUSE00000536631 Chr5:125517644..125517746 GGATGTCAGTCCAGCTTCGT Chr5:125517726..125517745 60.27 55
upstream ENSMUSE00000687723 Chr5:125517432..125517536 TCAGTGGAGTGAAGCAGGAA Chr5:125517511..125517530 59.54 50
upstream ENSMUSE00000389863 Chr5:125517191..125517288 No primer for this exon

*** Putative Vector Insertion (Chr 5: 125516497 - 125517190) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000318514 Chr5:125516346..125516496 ATAGGACGTGGCCTTTCTTG Chr5:125516333..125516352 59.19 50
downstream ENSMUSE00000318507 Chr5:125514726..125514866 GAGCACTGTGACACGGACAT Chr5:125514820..125514839 59.74 55
downstream ENSMUSE00000189248 Chr5:125514354..125514434 GATGTGATGCTGCTCCTTGA Chr5:125514351..125514370 59.95 50
downstream ENSMUSE00000189267 Chr5:125513696..125513991 CGCCGTAAGTAGTCCTCCTG Chr5:125513924..125513943 59.89 60
downstream ENSMUSE00000189298 Chr5:125512385..125512739 CTGACCGGCTCTTCAGACTC Chr5:125512540..125512559 60.13 60
downstream ENSMUSE00000318482 Chr5:125511056..125511277 CGGGGTGTAGATGTCAGCTT Chr5:125511201..125511220 60.13 55
downstream ENSMUSE00000318478 Chr5:125510342..125510596 TGCTGCGAGGTGATGTAGTC Chr5:125510427..125510446 60.02 55
downstream ENSMUSE00000318473 Chr5:125509490..125509639 GGACAGCGGTGAGCTACTGT Chr5:125509472..125509491 60.48 60
downstream ENSMUSE00000189277 Chr5:125509252..125509383 GGATGGACTTGTCTCGTTCC Chr5:125509275..125509294 59.51 55
downstream ENSMUSE00000536617 Chr5:125508991..125509168 No primer for this exon
downstream ENSMUSE00000370521 Chr5:125508982..125509168 No primer for this exon
downstream ENSMUSE00000189288 Chr5:125507172..125507587 GGGTAGGGTAGACCCCTTCA Chr5:125507468..125507487 60.18 60
downstream ENSMUSE00000318455 Chr5:125506022..125506174 CCTTCCAAGTGGCTCTTCTC Chr5:125506023..125506042 59.01 55
downstream ENSMUSE00000189261 Chr5:125505788..125505933 CTGGAGGAGTGGGCTAGATG Chr5:125505823..125505842 59.82 60
downstream ENSMUSE00000189273 Chr5:125505379..125505572 TGGGAGGTAGAGGTCACTGG Chr5:125505413..125505432 60.1 60
downstream ENSMUSE00000189254 Chr5:125504503..125504652 TCGATACAGCAGTGGGTACG Chr5:125504504..125504523 59.74 55
downstream ENSMUSE00000189259 Chr5:125503871..125504016 CCTGCTTCTTCGACTTCACC Chr5:125503897..125503916 59.99 55
downstream ENSMUSE00000189270 Chr5:125503241..125503294 No primer for this exon
downstream ENSMUSE00000189278 Chr5:125500189..125500416 GGCATTCAGAGGGTTAAAAGC Chr5:125500243..125500263 60.09 47.62
downstream ENSMUSE00000189242 Chr5:125499181..125499360 CTTTTCGGCTGCTAGGTCTG Chr5:125499291..125499310 60.15 55
downstream ENSMUSE00000420064 Chr5:125498205..125498718 AAAGGGTTGTAGGGGAATGG Chr5:125498669..125498688 60.05 50
downstream ENSMUSE00000536607 Chr5:125497532..125498718 AAAGGGTTGTAGGGGAATGG Chr5:125498669..125498688 60.05 50
downstream ENSMUSE00000687706 Chr5:125497525..125498718 AAAGGGTTGTAGGGGAATGG Chr5:125498669..125498688 60.05 50
downstream ENSMUSE00000687702 Chr5:125497523..125498718 AAAGGGTTGTAGGGGAATGG Chr5:125498669..125498688 60.05 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATCGCCTTGCAGCACATC Chr5:125517119..125517139 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGAGGCTCTATCACCCACGTA Chr5:125517186..125517208 61.56 54.54 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029478