Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI32838
Trapped Gene
Nsf (ENSMUSG00000034187)
Vector Insertion
Chr 11: 103792389 - 103815324
Public Clones (sanger) (sanger) (sanger) (sanger) (sanger) 5SE152G01 (ggtc)
3SE152G01 (ggtc) IST14840D7 (tigm) IST14988B9 (tigm) IST13045B12 (tigm)
IST14952C1 (tigm) IST11386C9 (tigm) IST10672G7 (tigm) IST12470A12 (tigm)
IST11713A10 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000661191 (Chr11:103815284..103815323 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000661191 (Chr11:103815284..103815323 -)
Downstram Exon
ENSMUSE00000671821 (Chr11:103792390..103792437 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon CAACTGCATAAAGGCTTTCCA Chr11:103792372..103792392 60.25 42.86

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

*** Putative Vector Insertion (Chr 11: 103792389 - 103815324) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000671823 Chr11:103792385..103792396 No primer for this exon
downstream ENSMUSE00000227092 Chr11:103792044..103792129 CAACCGCACAGTTGCTTAAA Chr11:103792050..103792069 59.91 45
downstream ENSMUSE00000227084 Chr11:103790058..103790157 GGACGTCCTCACCATCACAT Chr11:103790114..103790133 60.82 55
downstream ENSMUSE00000227079 Chr11:103787462..103787501 No primer for this exon
downstream ENSMUSE00000227072 Chr11:103777820..103777986 GAGAAGGCCTGGTTGTTGAA Chr11:103777811..103777830 60.23 50
downstream ENSMUSE00000227066 Chr11:103775115..103775222 GATCCATGGCTTCAATGTCC Chr11:103775137..103775156 60.29 50
downstream ENSMUSE00000227060 Chr11:103774630..103774705 GAGCGACGAATTTTCTGCTT Chr11:103774618..103774637 59.6 45
downstream ENSMUSE00000227055 Chr11:103771757..103771912 GATGATGGACTGGCGATTTT Chr11:103771853..103771872 59.9 45
downstream ENSMUSE00000671819 Chr11:103770740..103771912 GCATGGACGACGACAATATG Chr11:103771420..103771439 59.96 50
downstream ENSMUSE00000227052 Chr11:103744056..103744255 GGGGGTCCGTATAACAGGAT Chr11:103744194..103744213 59.9 55
downstream ENSMUSE00000227049 Chr11:103734459..103734624 CAAGCCACTGTTAGCACCAA Chr11:103734582..103734601 59.9 50
downstream ENSMUSE00000227046 Chr11:103733905..103733979 GTCGAAGGAGAGCTTCGTCT Chr11:103733913..103733932 58.77 55
downstream ENSMUSE00000227040 Chr11:103733473..103733660 TGGAGTCGACCCTTCTCATC Chr11:103733611..103733630 60.2 55
downstream ENSMUSE00000227033 Chr11:103724553..103724648 TATCGTTCTCCAGGGAAGCA Chr11:103724539..103724558 60.73 50
downstream ENSMUSE00000227024 Chr11:103723207..103723363 CCGGTCACTGTTTTTCGTTT Chr11:103723213..103723232 60.01 45
downstream ENSMUSE00000227017 Chr11:103720209..103720342 CTGTCTCGGAGAAGCCAATC Chr11:103720210..103720229 59.95 55
downstream ENSMUSE00000227011 Chr11:103709308..103709374 TCAATGTCATCCACGACCAC Chr11:103709297..103709316 60.39 50
downstream ENSMUSE00000227000 Chr11:103707688..103707767 AGGCGCCTTTTTCAGTAACA Chr11:103707672..103707691 59.88 45
downstream ENSMUSE00000226987 Chr11:103689746..103689880 TGGTCCCGATGATAAGAAGC Chr11:103689831..103689850 60.04 50
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 AAGGCCTCATAATCGCCTTG Chr11:103809262..103809282 61.45 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTTTCTGAGTAGAGCCCCATC Chr11:103806277..103806299 61.46 54.54 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034187