Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1630
Trapped Gene
Arcn1 (ENSMUSG00000032096)
Vector Insertion
Chr 9: 44568309 - 44575752
Public Clones AY0087 (sanger) YHC439 (baygenomics)
Private Clones OST194628 (lexicon) OST110782 (lexicon) OST41305 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000700344 (Chr9:44575753..44575896 -)
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
ENSMUSE00000700344 (Chr9:44575753..44575896 -)
Downstram Exon
ENSMUSE00000370160 (Chr9:44568045..44568308 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon ACAATAGCCTTTCCCGCTTT Chr9:44568240..44568259 60.1 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000700344 Chr9:44575753..44575896 No primer for this exon

*** Putative Vector Insertion (Chr 9: 44568309 - 44575752) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000370160 Chr9:44568045..44568308 ACAATAGCCTTTCCCGCTTT Chr9:44568240..44568259 60.1 45
downstream ENSMUSE00000216521 Chr9:44566964..44567143 TCCTCTAAGGCTCGGCAATA Chr9:44567093..44567112 59.94 50
downstream ENSMUSE00000216517 Chr9:44566644..44566849 GCCTTAGCCTCACGTTCTTG Chr9:44566805..44566824 60.01 55
downstream ENSMUSE00000216518 Chr9:44565203..44565367 TAGGTGGAGCATGCACTTTG Chr9:44565194..44565213 59.86 50
downstream ENSMUSE00000216515 Chr9:44560193..44560358 CTGTAGCTGCACCCCTTTCT Chr9:44560171..44560190 59.5 55
downstream ENSMUSE00000216512 Chr9:44559299..44559446 TCTGGGTTTTTCAAGCCAAT Chr9:44559360..44559379 59.55 40
downstream ENSMUSE00000216513 Chr9:44558408..44558516 CACAGCCATTTCCACTTTCC Chr9:44558459..44558478 60.49 50
downstream ENSMUSE00000402776 Chr9:44553501..44553705 GGCACCACTCCAACGTATTT Chr9:44553601..44553620 59.86 50
downstream ENSMUSE00000637376 Chr9:44550224..44552099 CTTCAGCAACTGATCGTCCA Chr9:44550717..44550736 59.98 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTGGACAGGTAATCGCCTTG Chr9:44569690..44569710 60.52 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATCTGTAGTGGACAGGCGTGA Chr9:44569696..44569717 60.73 52.38 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032096