Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10017
Trapped Gene
Depdc5 (ENSMUSG00000037426)
Vector Insertion
Chr 5: 33318194 - 33322033
Public Clones XE268 (baygenomics) XE269 (baygenomics) XE192 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 88% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000246556 (Chr5:33317966..33318193 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTAGCCGAAGTTTTGGAGGA Chr5:33318149..33318168 59.82 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000246556 (Chr5:33317966..33318193 +)
Downstram Exon
ENSMUSE00000246364 (Chr5:33322034..33322203 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTAGCCGAAGTTTTGGAGGA Chr5:33318149..33318168 59.82 45 TCACTGCCATCCAGTGTAGC Chr5:33322183..33322202 59.86 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000719988 Chr5:33206355..33206392 No primer for this exon
upstream ENSMUSE00000548842 Chr5:33206370..33206470 CTGGTTCCTAGAGCCCTGGT Chr5:33206421..33206440 60.64 60
upstream ENSMUSE00000709217 Chr5:33206383..33206470 CTGGTTCCTAGAGCCCTGGT Chr5:33206421..33206440 60.64 60
upstream ENSMUSE00000548597 Chr5:33206426..33206470 No primer for this exon
upstream ENSMUSE00000548840 Chr5:33206659..33206961 GTTAGTGGACCGCGAGTCAT Chr5:33206813..33206832 60.14 55
upstream ENSMUSE00000548839 Chr5:33207226..33207348 GCAAGATGACTTCCCTGCTC Chr5:33207236..33207255 59.96 55
upstream ENSMUSE00000713002 Chr5:33207226..33207348 GCAAGATGACTTCCCTGCTC Chr5:33207236..33207255 59.96 55
upstream ENSMUSE00000712196 Chr5:33207236..33207348 GCAAGATGACTTCCCTGCTC Chr5:33207236..33207255 59.96 55
upstream ENSMUSE00000246530 Chr5:33210623..33210710 AGATTGCTCACCCCAATGAT Chr5:33210683..33210702 59.37 45
upstream ENSMUSE00000246520 Chr5:33211470..33211516 TCCTTTGCTTTTGCAAGTCA Chr5:33211470..33211489 59.58 40
upstream ENSMUSE00000548645 Chr5:33217931..33218016 No primer for this exon
upstream ENSMUSE00000246508 Chr5:33219719..33219802 GGGGATATGTGGCGACTAAA Chr5:33219773..33219792 59.78 50
upstream ENSMUSE00000699470 Chr5:33219719..33219754 TGACTCTTGACCTGGTGGAA Chr5:33219723..33219742 59.23 50
upstream ENSMUSE00000246498 Chr5:33221277..33221326 AAGTGGAATTTGCTGGCATC Chr5:33221305..33221324 60.08 45
upstream ENSMUSE00000460817 Chr5:33221285..33221326 AAGTGGAATTTGCTGGCATC Chr5:33221305..33221324 60.08 45
upstream ENSMUSE00000246488 Chr5:33229628..33229697 AGCTGTGGGTCAAGAATGAGA Chr5:33229642..33229662 59.86 47.62
upstream ENSMUSE00000246481 Chr5:33236024..33236102 CGTTCTACGTCGGCTATGGT Chr5:33236033..33236052 60.15 55
upstream ENSMUSE00000246476 Chr5:33238529..33238590 CCTCGCCGACCTGTTTACTA Chr5:33238563..33238582 60.26 55
upstream ENSMUSE00000719751 Chr5:33238529..33238583 CCTCGCCGACCTGTTTACTA Chr5:33238563..33238582 60.26 55
upstream ENSMUSE00000246470 Chr5:33240528..33240597 CTGTGGTCCTGTTTTCCAGA Chr5:33240553..33240572 58.69 50
upstream ENSMUSE00000246463 Chr5:33241641..33241713 CCTGAAATAAACCGAGCTTCA Chr5:33241649..33241669 59.35 42.86
upstream ENSMUSE00000246456 Chr5:33244105..33244208 GGACTTCACTCCTCGTGACC Chr5:33244137..33244156 59.69 60
upstream ENSMUSE00000246450 Chr5:33244479..33244553 GGCCATCAACTTGTCATTCA Chr5:33244531..33244550 59.5 45
upstream ENSMUSE00000246441 Chr5:33246426..33246560 TTGAAGTGGACCGCCTACTC Chr5:33246507..33246526 60.26 55
upstream ENSMUSE00000246433 Chr5:33246924..33246985 TAGTGTGCATGGGAGAGCAG Chr5:33246939..33246958 60.01 55
upstream ENSMUSE00000246426 Chr5:33247108..33247181 GGATTCTCGACTGGGTGATG Chr5:33247131..33247150 60.47 55
upstream ENSMUSE00000384063 Chr5:33253106..33253175 ACACATCCAAAAGCCAGCTC Chr5:33253111..33253130 60.26 50
upstream ENSMUSE00000351488 Chr5:33254858..33254894 GAAAACCAAAAATGGTCGTGA Chr5:33254869..33254889 59.83 38.1
upstream ENSMUSE00000361342 Chr5:33255749..33255869 TGATGCCTACGATGCTCAAG Chr5:33255801..33255820 59.97 50
upstream ENSMUSE00000391397 Chr5:33260574..33260794 CAAGAGCACCAACATCCTGA Chr5:33260709..33260728 59.83 50
upstream ENSMUSE00000405364 Chr5:33266811..33267014 TGATAGAACCCCCACAGAGG Chr5:33266826..33266845 59.92 55
upstream ENSMUSE00000246399 Chr5:33269539..33269674 TTGGAGTTGGCATACCATGA Chr5:33269643..33269662 59.92 45
upstream ENSMUSE00000246392 Chr5:33270494..33270588 CTTCAGTGGAACGGAAGAGC Chr5:33270536..33270555 59.99 55
upstream ENSMUSE00000246385 Chr5:33276599..33276664 CCCAGAACAAGGACTCCCTA Chr5:33276614..33276633 59.13 55
upstream ENSMUSE00000548616 Chr5:33280170..33280353 CACAGTTGGAGTGGATTGGA Chr5:33280213..33280232 59.52 50
upstream ENSMUSE00000382712 Chr5:33280197..33280353 CACAGTTGGAGTGGATTGGA Chr5:33280213..33280232 59.52 50
upstream ENSMUSE00000246369 Chr5:33280794..33280954 AGTTCATCTGCCAGCGTCTC Chr5:33280841..33280860 60.56 55
upstream ENSMUSE00000246639 Chr5:33285881..33285998 No primer for this exon
upstream ENSMUSE00000413129 Chr5:33286620..33286787 GAACGGCTCGAGGAATACAA Chr5:33286717..33286736 60.21 50
upstream ENSMUSE00000350234 Chr5:33287572..33287791 AGAGGGCTTAAATCGCATCC Chr5:33287740..33287759 60.55 50
upstream ENSMUSE00000246610 Chr5:33289283..33289416 ACACTCTCTCGAGGCAGCAG Chr5:33289330..33289349 60.9 60
upstream ENSMUSE00000246598 Chr5:33298502..33298607 ACTGTGCACGGAAAAAGCTC Chr5:33298524..33298543 60.44 50
upstream ENSMUSE00000548576 Chr5:33298778..33298949 TCCACACAAGCCTGTACCTTT Chr5:33298899..33298919 59.65 47.62
upstream ENSMUSE00000699441 Chr5:33298778..33298804 No primer for this exon
upstream ENSMUSE00000548614 Chr5:33301930..33301995 GGGGCCTTCTTTATGGAGTT Chr5:33301933..33301952 59.42 50
upstream ENSMUSE00000246589 Chr5:33307281..33307432 AGGCAACAACCAGACCTTTG Chr5:33307358..33307377 60.15 50
upstream ENSMUSE00000405684 Chr5:33310380..33310457 TACCCTGGTGGAGATTCTGG Chr5:33310419..33310438 59.92 55
upstream ENSMUSE00000246572 Chr5:33311288..33311420 TGCTGAGGTCGTACACTGGT Chr5:33311345..33311364 59.34 55
upstream ENSMUSE00000246563 Chr5:33316466..33316574 CATGGCGGACCTTCATCTAT Chr5:33316509..33316528 59.92 50
upstream ENSMUSE00000246556 Chr5:33317966..33318193 TTAGCCGAAGTTTTGGAGGA Chr5:33318149..33318168 59.82 45

*** Putative Vector Insertion (Chr 5: 33318194 - 33322033) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000246364 Chr5:33322034..33322203 TCACTGCCATCCAGTGTAGC Chr5:33322183..33322202 59.86 55
downstream ENSMUSE00000246359 Chr5:33326508..33326679 TAGCTTTTCGATGCCAACCT Chr5:33326535..33326554 59.85 45
downstream ENSMUSE00000246355 Chr5:33329585..33329645 CAATGGCTTCCTGGAAAAGA Chr5:33329641..33329660 60.18 45
downstream ENSMUSE00000601014 Chr5:33333391..33333473 No primer for this exon
downstream ENSMUSE00000601015 Chr5:33333391..33333473 No primer for this exon
downstream ENSMUSE00000413171 Chr5:33333588..33334209 ACTCACTCCCACGGACAATC Chr5:33334124..33334143 59.97 55
downstream ENSMUSE00000548673 Chr5:33333588..33334209 ACTCACTCCCACGGACAATC Chr5:33334124..33334143 59.97 55
downstream ENSMUSE00000710102 Chr5:33333588..33334317 ACTCACTCCCACGGACAATC Chr5:33334124..33334143 59.97 55
downstream ENSMUSE00000710946 Chr5:33333588..33334310 ACTCACTCCCACGGACAATC Chr5:33334124..33334143 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGTGGTTAATCGCCTTGCAG Chr5:33318239..33318259 60.27 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGGAGTCTGGGGATAGCAG Chr5:33318206..33318226 60.21 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037426