Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31065
Trapped Gene
Dnahc5 (ENSMUSG00000022262)
Vector Insertion
Chr 15: 28182349 - 28193306
Public Clones (sanger) IST11137C8 (tigm) IST12404E8 (tigm) IST13707H3 (tigm) IST15004A10 (tigm)
IST14677C12 (tigm) IST14464C3 (tigm) IST13777A7 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 17% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000485900 (Chr15:28182177..28182348 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCCTGAATATTGGGGGCTAT Chr15:28182304..28182323 60 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000485900 (Chr15:28182177..28182348 +)
Downstram Exon
ENSMUSE00000485073 (Chr15:28193307..28193452 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCCTGAATATTGGGGGCTAT Chr15:28182304..28182323 60 50 TTCACAAGTCAGGGGGTCAT Chr15:28193434..28193453 60.36 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000467310 Chr15:28133521..28133790 ATGTTTAGGATCGGCAGACG Chr15:28133734..28133753 60.1 50
upstream ENSMUSE00000260313 Chr15:28148850..28148984 GGCGGCATGACTATCTGTTT Chr15:28148896..28148915 60.1 50
upstream ENSMUSE00000260308 Chr15:28153950..28154034 GTTGGTGGACTCCGTCATCT Chr15:28153977..28153996 59.97 55
upstream ENSMUSE00000260302 Chr15:28159254..28159414 GCCATTACGCCTGAGAACAT Chr15:28159388..28159407 60.1 50
upstream ENSMUSE00000260293 Chr15:28160151..28160372 CACGTTAGACACGGCAGATG Chr15:28160165..28160184 60.32 55
upstream ENSMUSE00000488426 Chr15:28162912..28163049 TGAAGGAACCCACGGACTAC Chr15:28162952..28162971 59.97 55
upstream ENSMUSE00000487407 Chr15:28164000..28164176 GCACTGGAAACAAAGGCTCT Chr15:28164065..28164084 59.48 50
upstream ENSMUSE00000490305 Chr15:28165459..28165572 No primer for this exon
upstream ENSMUSE00000489762 Chr15:28166374..28166481 No primer for this exon
upstream ENSMUSE00000480386 Chr15:28168266..28168388 ATCACCAACAATGGGACTGC Chr15:28168302..28168321 60.79 50
upstream ENSMUSE00000479552 Chr15:28169574..28169789 CGACGTCTGGCCAAGATAAT Chr15:28169685..28169704 60.1 50
upstream ENSMUSE00000482407 Chr15:28172412..28172519 TTTTGCAAGCGGATTAATGA Chr15:28172493..28172512 59.29 35
upstream ENSMUSE00000477249 Chr15:28175417..28175502 CAAGCTCTAAGCACGCTGAA Chr15:28175471..28175490 59.51 50
upstream ENSMUSE00000484454 Chr15:28176003..28176324 CCAGAATTTTGCGACTGACA Chr15:28176051..28176070 59.84 45
upstream ENSMUSE00000483570 Chr15:28177526..28177732 AAGCGGGACATGTTCAAAAA Chr15:28177694..28177713 60.48 40
upstream ENSMUSE00000485900 Chr15:28182177..28182348 CCCTGAATATTGGGGGCTAT Chr15:28182304..28182323 60 50

*** Putative Vector Insertion (Chr 15: 28182349 - 28193306) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000485073 Chr15:28193307..28193452 TTCACAAGTCAGGGGGTCAT Chr15:28193434..28193453 60.36 50
downstream ENSMUSE00000503272 Chr15:28199048..28199210 GTTTTCGGCTGCTTCTTCAG Chr15:28199173..28199192 60.13 50
downstream ENSMUSE00000506060 Chr15:28200049..28200282 CCCGGAAGTTAATCATGTGG Chr15:28200285..28200304 60.18 50
downstream ENSMUSE00000505054 Chr15:28201781..28201971 TCATAGCGATGTTGGGAATG Chr15:28201870..28201889 59.5 45
downstream ENSMUSE00000499748 Chr15:28202060..28202147 CTCCACCTCAGCGTCTGAAT Chr15:28202134..28202153 60.41 55
downstream ENSMUSE00000500386 Chr15:28208269..28208402 GGAGCTGATGACTGTGCTGA Chr15:28208396..28208415 60.15 55
downstream ENSMUSE00000476717 Chr15:28218809..28219010 GGAACCCACACGGATGTATT Chr15:28218997..28219016 59.53 50
downstream ENSMUSE00000479154 Chr15:28219810..28220045 AAGTCGGTGGAGATCTGCTG Chr15:28220029..28220048 60.41 55
downstream ENSMUSE00000478250 Chr15:28223331..28223549 AGCAGCTTCTCCCAAGCATA Chr15:28223428..28223447 60.12 50
downstream ENSMUSE00000503967 Chr15:28224673..28224735 GCTTCAATCCACTTGCCATC Chr15:28224703..28224722 60.61 50
downstream ENSMUSE00000494771 Chr15:28224985..28225223 TGTTCACGTCTGACCAAAGG Chr15:28225186..28225205 59.72 50
downstream ENSMUSE00000497618 Chr15:28226763..28227003 ATCCTCTGCCAGTGTCGTTC Chr15:28226906..28226925 60.27 55
downstream ENSMUSE00000497027 Chr15:28228836..28229035 TCTCTCTCCTTCACGGCACT Chr15:28228870..28228889 60.13 55
downstream ENSMUSE00000492070 Chr15:28232141..28232294 GTCTCCTCCCACGAAGACAG Chr15:28232276..28232295 59.83 60
downstream ENSMUSE00000499370 Chr15:28234341..28234504 CTGGCAGATTTCCAACTGGT Chr15:28234493..28234512 60.11 50
downstream ENSMUSE00000495828 Chr15:28236988..28237144 CAAACACGTTCAGCAAATGG Chr15:28237115..28237134 60.15 45
downstream ENSMUSE00000520540 Chr15:28240894..28241106 CTCCCGAGAGGAGATTGACA Chr15:28240932..28240951 60.34 55
downstream ENSMUSE00000514837 Chr15:28241914..28242138 AGCTCAGGTCCTTCGTGGTA Chr15:28242070..28242089 59.87 55
downstream ENSMUSE00000493988 Chr15:28243495..28243667 GTAGGGCTCTTGACGTGCAT Chr15:28243523..28243542 60.28 55
downstream ENSMUSE00000519335 Chr15:28256275..28256453 TTTGAATATCCGCCCAAGTC Chr15:28256455..28256474 59.9 45
downstream ENSMUSE00000125105 Chr15:28256946..28257133 GGGCTGCAACTGACAGAACT Chr15:28257026..28257045 60.45 55
downstream ENSMUSE00000125107 Chr15:28257477..28257671 CACAGCTGGTAGAGCGTGAA Chr15:28257652..28257671 60.2 55
downstream ENSMUSE00000472198 Chr15:28261460..28261594 CTGACAGAATGTTGCGGAGA Chr15:28261499..28261518 59.98 50
downstream ENSMUSE00000513798 Chr15:28262780..28262887 ATAGCCTGCCTTGTCCAAAA Chr15:28262860..28262879 59.71 45
downstream ENSMUSE00000507360 Chr15:28265323..28265476 TCTGCGTTTCAAACAACTGG Chr15:28265395..28265414 59.88 45
downstream ENSMUSE00000506413 Chr15:28270036..28270182 TCGAGTCGACCAAACATCTG Chr15:28270114..28270133 59.83 50
downstream ENSMUSE00000470330 Chr15:28273190..28273431 CCAGTCGAGGACTGAGGAAC Chr15:28273419..28273438 59.83 60
downstream ENSMUSE00000465604 Chr15:28275492..28275668 ACAGGTCCGGGAAAGTCTCT Chr15:28275570..28275589 60.11 55
downstream ENSMUSE00000464944 Chr15:28276526..28276727 ACACTCCACATCATGGCAAA Chr15:28276596..28276615 59.97 45
downstream ENSMUSE00000467698 Chr15:28279528..28279670 CCACATTTGGCACAAGGATA Chr15:28279623..28279642 59.4 45
downstream ENSMUSE00000474276 Chr15:28280332..28280466 GTCGCCGAAGAAAAGTTCAG Chr15:28280450..28280469 59.99 50
downstream ENSMUSE00000469548 Chr15:28295293..28295415 CCCCATTCGTTGATTACAGG Chr15:28295411..28295430 60.18 50
downstream ENSMUSE00000468546 Chr15:28295899..28296112 TCTTCAAGCGCTGTGGTATG Chr15:28296055..28296074 60.01 50
downstream ENSMUSE00000471318 Chr15:28297441..28297664 GTAGTAGCCTGCCCCAATCA Chr15:28297466..28297485 60.1 55
downstream ENSMUSE00000442735 Chr15:28300110..28300308 CAGCCTTATCGAACCAGGTC Chr15:28300203..28300222 59.69 55
downstream ENSMUSE00000488236 Chr15:28301998..28302170 ATGCGATTGGCTCATAAAGC Chr15:28302057..28302076 60.2 45
downstream ENSMUSE00000487067 Chr15:28308086..28308216 CGATGAATGAAGCCAACCTT Chr15:28308185..28308204 60.07 45
downstream ENSMUSE00000490087 Chr15:28313331..28313484 TCTTCCATCAGGTTCGAGGT Chr15:28313363..28313382 59.65 50
downstream ENSMUSE00000466101 Chr15:28313963..28314230 ATCAATTTCATCCCGAGCAA Chr15:28313998..28314017 60.41 40
downstream ENSMUSE00000461347 Chr15:28317516..28317747 TCCTTCTTGATCTCCGCTGT Chr15:28317576..28317595 59.95 50
downstream ENSMUSE00000460279 Chr15:28320198..28320312 TGCAGCTCCTTCTCTTTTCC Chr15:28320290..28320309 59.69 50
downstream ENSMUSE00000463171 Chr15:28320463..28320639 GCACCTCAGCTTTGACCTTC Chr15:28320523..28320542 60 55
downstream ENSMUSE00000481149 Chr15:28326806..28327009 GCCTTTGTCCACGTCAATTT Chr15:28326943..28326962 59.98 45
downstream ENSMUSE00000480272 Chr15:28331542..28331721 GGCCGTCTCGATGTTGTAGT Chr15:28331631..28331650 60.14 55
downstream ENSMUSE00000486568 Chr15:28333158..28333295 GCCATGGCCTGTTCATACTC Chr15:28333288..28333307 60.49 55
downstream ENSMUSE00000477782 Chr15:28338036..28338171 ACGAGCCGTTTAGTTTGTGC Chr15:28338172..28338191 60.31 50
downstream ENSMUSE00000502356 Chr15:28338739..28339055 GCAGGTCTCGAAACTCTTGG Chr15:28338810..28338829 59.99 55
downstream ENSMUSE00000505515 Chr15:28339601..28339756 CAACATCCTCGATGAGCAAA Chr15:28339688..28339707 59.8 45
downstream ENSMUSE00000493920 Chr15:28341261..28341443 GATGGAGGTCCGAGCACTTA Chr15:28341374..28341393 60.22 55
downstream ENSMUSE00000492737 Chr15:28349515..28349758 CCGGGCTGAGTTAATTTGAA Chr15:28349745..28349764 60.07 45
downstream ENSMUSE00000519096 Chr15:28350720..28350834 GAAACTGACGGAGCGAAGTC Chr15:28350809..28350828 60 55
downstream ENSMUSE00000498404 Chr15:28351320..28351510 CTCGGGCAGCATACTTGAAT Chr15:28351408..28351427 60.24 50
downstream ENSMUSE00000491901 Chr15:28365925..28366046 TGATGGCTTAGGAGGACAGG Chr15:28365971..28365990 60.21 55
downstream ENSMUSE00000259400 Chr15:28367854..28368003 CGTCTGAAGCAGTCGAGAGA Chr15:28367960..28367979 59.44 55
downstream ENSMUSE00000259540 Chr15:28373837..28374082 AGGAGGCAGATGAGTGGTGT Chr15:28373952..28373971 59.71 55
downstream ENSMUSE00000259609 Chr15:28374745..28374964 GGCTCATTGGCAAACTTGAT Chr15:28374926..28374945 60.08 45
downstream ENSMUSE00000259533 Chr15:28378038..28378243 AGGGATATTCCACCCCAGAG Chr15:28378168..28378187 60.15 55
downstream ENSMUSE00000259597 Chr15:28378905..28379108 TCATGTAGCGGACAGTGGTC Chr15:28378938..28378957 59.71 55
downstream ENSMUSE00000259592 Chr15:28381073..28381288 CTGGATGCCCAGGATAGTGT Chr15:28381186..28381205 59.95 55
downstream ENSMUSE00000474691 Chr15:28382956..28383168 GGCTGAGTACCCTCTGCATC Chr15:28383049..28383068 59.83 60
downstream ENSMUSE00000259458 Chr15:28388303..28388455 CTGTCGCATCGCAGTTAAGA Chr15:28388458..28388477 60.16 50
downstream ENSMUSE00000468029 Chr15:28388874..28389105 TGACAGGCATCAGCTCAAAA Chr15:28389084..28389103 60.54 45
downstream ENSMUSE00000473678 Chr15:28400112..28401800 CGGTACAGACCCCACACTTT Chr15:28400875..28400894 59.88 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CGGCATCTAGTGTTGAACAGA Chr15:28182301..28182322 58.94 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGGCATCTAGTGTTGAACAGA Chr15:28182301..28182322 58.94 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000022262