Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI20910
Trapped Gene
Phf21a (ENSMUSG00000058318)
Vector Insertion
Chr 2: 92197177 - 92198850
Public Clones not available
Private Clones OST348484 (lexicon)
Severity of mutation (?) Insertion after 79% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000299203 (Chr2:92197021..92197176 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TCCCGTGTGTATCATCTGGA Chr2:92197090..92197109 59.92 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000299203 (Chr2:92197021..92197176 +)
Downstram Exon
ENSMUSE00000299198 (Chr2:92198851..92198926 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TCCCGTGTGTATCATCTGGA Chr2:92197090..92197109 59.92 50 TGCTTTGTAGGCGATGTAGG Chr2:92198928..92198947 58.94 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000687386 Chr2:91933274..91933310 AAAAACTGAGCCCACTACCTCA Chr2:91933287..91933308 60.17 45.46
upstream ENSMUSE00000642532 Chr2:92024263..92024509 CCCTCCCCATGAAGAAGAGT Chr2:92024406..92024425 60.45 55
upstream ENSMUSE00000687368 Chr2:92024364..92024509 CCCTCCCCATGAAGAAGAGT Chr2:92024406..92024425 60.45 55
upstream ENSMUSE00000687365 Chr2:92024433..92024509 CTCAGAGTTCCTGCCTCCAG Chr2:92024456..92024475 60.13 60
upstream ENSMUSE00000687364 Chr2:92025640..92025745 TCTCTCTTCGCTCGCTCTCT Chr2:92025682..92025701 59.73 55
upstream ENSMUSE00000687363 Chr2:92026708..92026766 No primer for this exon
upstream ENSMUSE00000687372 Chr2:92054206..92054246 GGACTGGAGAGCTGAAGGAG Chr2:92054207..92054226 59.13 60
upstream ENSMUSE00000687367 Chr2:92055621..92055732 AGGGAGCCCACTACCTCATAA Chr2:92055711..92055731 59.97 52.38
upstream ENSMUSE00000710902 Chr2:92061627..92061772 AACGGAGGCTGAAGACACTG Chr2:92061659..92061678 60.44 55
upstream ENSMUSE00000715490 Chr2:92061627..92061772 AACGGAGGCTGAAGACACTG Chr2:92061659..92061678 60.44 55
upstream ENSMUSE00000687371 Chr2:92061629..92061772 AACGGAGGCTGAAGACACTG Chr2:92061659..92061678 60.44 55
upstream ENSMUSE00000599875 Chr2:92068606..92068638 AACTGGTTGCCCAAATGAAG Chr2:92068607..92068626 59.97 45
upstream ENSMUSE00000710004 Chr2:92068606..92068638 AACTGGTTGCCCAAATGAAG Chr2:92068607..92068626 59.97 45
upstream ENSMUSE00000717571 Chr2:92068606..92068638 AACTGGTTGCCCAAATGAAG Chr2:92068607..92068626 59.97 45
upstream ENSMUSE00000599874 Chr2:92070816..92070881 TTCATGAACTCCAAGCCAAA Chr2:92070838..92070857 59.25 40
upstream ENSMUSE00000687353 Chr2:92070816..92070881 TTCATGAACTCCAAGCCAAA Chr2:92070838..92070857 59.25 40
upstream ENSMUSE00000599873 Chr2:92160386..92160616 GCACCGCCTAGTCTAACTGC Chr2:92160590..92160609 60.04 60
upstream ENSMUSE00000687352 Chr2:92160386..92160616 GCACCGCCTAGTCTAACTGC Chr2:92160590..92160609 60.04 60
upstream ENSMUSE00000565030 Chr2:92167070..92167321 GCAGAGGCTGTCCAAATTGT Chr2:92167280..92167299 60.26 50
upstream ENSMUSE00000687358 Chr2:92167073..92167321 GCAGAGGCTGTCCAAATTGT Chr2:92167280..92167299 60.26 50
upstream ENSMUSE00000299255 Chr2:92168469..92168558 GGTTCAAGCAACACCTCCTC Chr2:92168471..92168490 59.7 55
upstream ENSMUSE00000447288 Chr2:92168472..92168558 CCTCAGCCCATCAAAGTACC Chr2:92168487..92168506 59.55 55
upstream ENSMUSE00000687351 Chr2:92168472..92168558 CCTCAGCCCATCAAAGTACC Chr2:92168487..92168506 59.55 55
upstream ENSMUSE00000599867 Chr2:92170672..92170965 CAGCTCACCAGCATTGTCAT Chr2:92170876..92170895 59.86 50
upstream ENSMUSE00000599872 Chr2:92170672..92170965 CAGCTCACCAGCATTGTCAT Chr2:92170876..92170895 59.86 50
upstream ENSMUSE00000299242 Chr2:92184701..92184799 AACAAGCAGAGAGCCGTACC Chr2:92184732..92184751 59.5 55
upstream ENSMUSE00000564996 Chr2:92184701..92184739 TTAAATCCCACCCAGAAGCA Chr2:92184705..92184724 60.44 45
upstream ENSMUSE00000565025 Chr2:92184705..92184741 TTAAATCCCACCCAGAAGCA Chr2:92184705..92184724 60.44 45
upstream ENSMUSE00000299234 Chr2:92188153..92188204 TCATGGTGTCTCTAGGGTTGG Chr2:92188163..92188183 59.97 52.38
upstream ENSMUSE00000643195 Chr2:92188178..92188204 No primer for this exon
upstream ENSMUSE00000299225 Chr2:92189035..92189114 GGTGTACAGTGGGGCTGTCT Chr2:92189084..92189103 60.03 60
upstream ENSMUSE00000299219 Chr2:92189545..92189605 CCTTAACAGCACAATGCATCC Chr2:92189568..92189588 60.52 47.62
upstream ENSMUSE00000299209 Chr2:92191766..92191788 AATGAGGAACACTGGCCAAA Chr2:92191768..92191787 60.49 45
upstream ENSMUSE00000447225 Chr2:92191858..92192021 CAAAATACAATGCGGTGCTG Chr2:92191867..92191886 60.13 45
upstream ENSMUSE00000687356 Chr2:92191989..92192021 No primer for this exon
upstream ENSMUSE00000299203 Chr2:92197021..92197176 TCCCGTGTGTATCATCTGGA Chr2:92197090..92197109 59.92 50

*** Putative Vector Insertion (Chr 2: 92197177 - 92198850) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000299198 Chr2:92198851..92198926 TGCTTTGTAGGCGATGTAGG Chr2:92198928..92198947 58.94 50
downstream ENSMUSE00000299191 Chr2:92199263..92199366 TTGTTCCCGCTCCTGTTTTA Chr2:92199330..92199349 60.61 45
downstream ENSMUSE00000643191 Chr2:92200326..92201050 AAACGGCTCCCAGTAAGGAT Chr2:92200981..92201000 59.96 50
downstream ENSMUSE00000687362 Chr2:92200326..92201058 AAACGGCTCCCAGTAAGGAT Chr2:92200981..92201000 59.96 50
downstream ENSMUSE00000687366 Chr2:92200326..92204822 CTTGAAGGACGTCATCAGCA Chr2:92203836..92203855 59.98 50
downstream ENSMUSE00000687369 Chr2:92200326..92201986 AAACGGCTCCCAGTAAGGAT Chr2:92200981..92201000 59.96 50
downstream ENSMUSE00000564995 Chr2:92200951..92201046 AAACGGCTCCCAGTAAGGAT Chr2:92200981..92201000 59.96 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTACTGGGGTGGATCACCTG Chr2:92197178..92197198 60.24 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTACTGGGGTGGATCACCTG Chr2:92197178..92197198 60.24 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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