Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29108
Trapped Gene
Hmgn1 (ENSMUSG00000040681)
Vector Insertion
Chr 16: 96348948 - 96349038
Public Clones not available
Private Clones OST8630 (lexicon)
Severity of mutation (?) Insertion after 16% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000401384 (Chr16:96349039..96349068 -)
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
ENSMUSE00000401384 (Chr16:96349039..96349068 -)
Downstram Exon
ENSMUSE00000348811 (Chr16:96348918..96348947 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000486012 Chr16:96349197..96349290 No primer for this exon
upstream ENSMUSE00000401384 Chr16:96349039..96349068 No primer for this exon

*** Putative Vector Insertion (Chr 16: 96348948 - 96349038) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000348811 Chr16:96348918..96348947 No primer for this exon
downstream ENSMUSE00000389240 Chr16:96348760..96348810 No primer for this exon
downstream ENSMUSE00000262291 Chr16:96346330..96346452 TGGTTTTCCGTCTCTCCATT Chr16:96346309..96346328 59.53 45
downstream ENSMUSE00000335749 Chr16:96343196..96344024 TCAGTCCCACCAATTCACAA Chr16:96343402..96343421 59.94 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTAATCGCCTTGCAGCACAT Chr16:96348968..96348988 61.69 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTGCTTTCTCCTGCAGGTTAGC Chr16:96349061..96349083 62.62 54.54 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040681