Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI18365
Trapped Gene
Nsf (ENSMUSG00000034187)
Vector Insertion
Chr 11: 103688639 - 103689745
Public Clones 5SE152D02 (ggtc)
Private Clones OST424892 (lexicon)
Severity of mutation (?) Insertion after 92% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000226987 (Chr11:103689746..103689880 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCTTCTTATCATCGGGACCA Chr11:103689853..103689872 60.04 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000226987 (Chr11:103689746..103689880 -)
Downstram Exon
ENSMUSE00000226980 (Chr11:103688525..103688638 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCTTCTTATCATCGGGACCA Chr11:103689853..103689872 60.04 50 CAATTGTGGTGCGTTCCTTA Chr11:103688577..103688596 59.58 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000661191 Chr11:103815284..103815323 No primer for this exon
upstream ENSMUSE00000671822 Chr11:103815284..103815338 No primer for this exon
upstream ENSMUSE00000671821 Chr11:103792390..103792437 No primer for this exon
upstream ENSMUSE00000671823 Chr11:103792385..103792396 No primer for this exon
upstream ENSMUSE00000227092 Chr11:103792044..103792129 TAAGCAACTGTGCGGTTGTG Chr11:103792070..103792089 60.9 50
upstream ENSMUSE00000227084 Chr11:103790058..103790157 ACGTCCCCCAATCACAAGTA Chr11:103790122..103790141 60.23 50
upstream ENSMUSE00000227079 Chr11:103787462..103787501 GGGCTGGACTTTCTATTGGAC Chr11:103787474..103787494 59.95 52.38
upstream ENSMUSE00000227072 Chr11:103777820..103777986 ACCCTTACGACACCGACAAG Chr11:103777877..103777896 60.03 55
upstream ENSMUSE00000227066 Chr11:103775115..103775222 CATCAGGCAAAAGGCAGAAG Chr11:103775115..103775134 60.9 50
upstream ENSMUSE00000227060 Chr11:103774630..103774705 GCCTGGTTGTTGGAAACAGT Chr11:103774676..103774695 60.01 50
upstream ENSMUSE00000227055 Chr11:103771757..103771912 AAAATCGCCAGTCCATCATC Chr11:103771875..103771894 59.9 45
upstream ENSMUSE00000671819 Chr11:103770740..103771912 GTAGCCGGCTGTGTCTTAGC Chr11:103770950..103770969 60.04 60
upstream ENSMUSE00000227052 Chr11:103744056..103744255 GTTATACGGACCCCCTGGTT Chr11:103744211..103744230 59.94 55
upstream ENSMUSE00000227049 Chr11:103734459..103734624 GTGGCTTGCACATCATCATC Chr11:103734592..103734611 60.09 50
upstream ENSMUSE00000227046 Chr11:103733905..103733979 GACCCGGAAGACTGGAAGTT Chr11:103733918..103733937 60.49 55
upstream ENSMUSE00000227040 Chr11:103733473..103733660 AGGGTCGACTCCAGATCCTT Chr11:103733626..103733645 60.07 55
upstream ENSMUSE00000227033 Chr11:103724553..103724648 AGAGGGGACTTCCTTGCTTC Chr11:103724575..103724594 59.82 55
upstream ENSMUSE00000227024 Chr11:103723207..103723363 GACCCGAGTCCTAGATGACG Chr11:103723273..103723292 59.68 60
upstream ENSMUSE00000227017 Chr11:103720209..103720342 CTTCTCCGAGACAGCCAAGT Chr11:103720226..103720245 59.6 55
upstream ENSMUSE00000227011 Chr11:103709308..103709374 GTGGTCGTGGATGACATTGA Chr11:103709319..103709338 60.39 50
upstream ENSMUSE00000227000 Chr11:103707688..103707767 CGGTTCTCCAACCTGGTATT Chr11:103707728..103707747 58.91 50
upstream ENSMUSE00000226987 Chr11:103689746..103689880 GCTTCTTATCATCGGGACCA Chr11:103689853..103689872 60.04 50

*** Putative Vector Insertion (Chr 11: 103688639 - 103689745) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000226980 Chr11:103688525..103688638 CAATTGTGGTGCGTTCCTTA Chr11:103688577..103688596 59.58 45
downstream ENSMUSE00000661190 Chr11:103685053..103685108 GGCCAAGAATTTCCTCACAC Chr11:103685051..103685070 59.53 50
downstream ENSMUSE00000671824 Chr11:103683099..103684573 GAGAGAGGCGGACACTTCAC Chr11:103684419..103684438 59.99 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACATTGCCACAGGAGAGCAG Chr11:103689762..103689782 61.42 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACATTGCCACAGGAGAGCAG Chr11:103689762..103689782 61.42 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCGCAAGCTTCTTATCATCG Chr11:103689857..103689877 60.87 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 AAAGATGTCCTGCCGTGACT Chr11:103689823..103689843 59.73 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034187