Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14594
Trapped Gene
Rnf220 (ENSMUSG00000028677)
Vector Insertion
Chr 4: 117162193 - 117169658
Public Clones FHCRC-GT-S17-1A1 (fhcrc) IST14886C7 (tigm) IST13540A12 (tigm) IST14604C7 (tigm)
IST13540A12 (tigm) IST14909D6 (tigm) IST12604D3 (tigm)
Private Clones OST332563 (lexicon) OST302037 (lexicon) OST194404 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000631419 (Chr4:117169288..117169657 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAAAGTGCGATCGTTCTCC Chr4:117169303..117169322 59.82 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000631419 (Chr4:117169288..117169657 -)
Downstram Exon
ENSMUSE00000416436 (Chr4:117162194..117162935 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAAAGTGCGATCGTTCTCC Chr4:117169303..117169322 59.82 50 AGGGAATGTGAACGTCCTTG Chr4:117162613..117162632 59.97 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000631419 Chr4:117169288..117169657 GAAAAGTGCGATCGTTCTCC Chr4:117169303..117169322 59.82 50
upstream ENSMUSE00000416436 Chr4:117162194..117162935 CACCAATGGCTCCTACACCT Chr4:117162614..117162633 59.99 55
upstream ENSMUSE00000705661 Chr4:117162194..117162818 CACCAATGGCTCCTACACCT Chr4:117162614..117162633 59.99 55

*** Putative Vector Insertion (Chr 4: 117162193 - 117169658) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000600443 Chr4:117047919..117048062 TGTCAGGATCCCTGTTGGAT Chr4:117047913..117047932 60.33 50
downstream ENSMUSE00000353420 Chr4:116980151..116980283 TGGCTGTCAAACAACGCTAC Chr4:116980228..116980247 59.91 50
downstream ENSMUSE00000600442 Chr4:116980151..116980283 TGGCTGTCAAACAACGCTAC Chr4:116980228..116980247 59.91 50
downstream ENSMUSE00000396426 Chr4:116972150..116972195 No primer for this exon
downstream ENSMUSE00000353812 Chr4:116968737..116968838 CCCTCTTGATGGAAGCAGAC Chr4:116968786..116968805 59.8 55
downstream ENSMUSE00000631418 Chr4:116961808..116962051 No primer for this exon
downstream ENSMUSE00000407394 Chr4:116961631..116961673 No primer for this exon
downstream ENSMUSE00000669899 Chr4:116961128..116961377 GGGCCGACTGATAACTCAAA Chr4:116961119..116961138 60.07 50
downstream ENSMUSE00000416114 Chr4:116958534..116958577 CATCTTGCTTCCTCCGTTTC Chr4:116958520..116958539 59.81 50
downstream ENSMUSE00000669898 Chr4:116958534..116958577 CATCTTGCTTCCTCCGTTTC Chr4:116958520..116958539 59.81 50
downstream ENSMUSE00000600441 Chr4:116958456..116958577 CATCTTGCTTCCTCCGTTTC Chr4:116958520..116958539 59.81 50
downstream ENSMUSE00000181244 Chr4:116957984..116958116 TATTCCTCAAAGCGGTTGCT Chr4:116958021..116958040 59.85 45
downstream ENSMUSE00000181245 Chr4:116950612..116950708 TCTGGGTTCTCTTTGCCACT Chr4:116950647..116950666 59.84 50
downstream ENSMUSE00000662304 Chr4:116950348..116950434 TCACCAGGCTCTTCTCCTGT Chr4:116950365..116950384 59.99 55
downstream ENSMUSE00000181246 Chr4:116950187..116950242 GGCCCATTTAGAGAACTCAGG Chr4:116950172..116950192 60.08 52.38
downstream ENSMUSE00000181242 Chr4:116949976..116950054 CTCAATGTCGCTGTTCTTGC Chr4:116949956..116949975 59.6 50
downstream ENSMUSE00000181248 Chr4:116945852..116945960 GATAGCTGCCGTTCAAGCTC Chr4:116945864..116945883 60.12 55
downstream ENSMUSE00000181243 Chr4:116945658..116945732 GACGTCAGAGGCATCGAGTA Chr4:116945685..116945704 58.99 55
downstream ENSMUSE00000600440 Chr4:116944532..116944980 GTGATGGTGTTGCACTGAGG Chr4:116944921..116944940 60.16 55
downstream ENSMUSE00000631417 Chr4:116944077..116944980 CGGCTCCAGAGTCCTCTATG Chr4:116944734..116944753 59.97 60
downstream ENSMUSE00000600439 Chr4:116944069..116944980 TGGTAGAGGGCAAAGTGTCC Chr4:116944506..116944525 60.11 55
downstream ENSMUSE00000705662 Chr4:116944068..116944980 CGGCTCCAGAGTCCTCTATG Chr4:116944734..116944753 59.97 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAGTGCCAGGCATTCTGTTG Chr4:117166666..117166686 61.24 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCCCAGAGTCCCTTAGTACCC Chr4:117166686..117166707 59.45 57.14 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GCGTGTGCGTACACAAGAGT Chr4:117166235..117166255 59.98 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 AGGAACGTGACTGGGAAAAC Chr4:117166221..117166241 59.04 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028677