Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9933
Trapped Gene
Arcn1 (ENSMUSG00000032096)
Vector Insertion
Chr 9: 44565368 - 44566643
Public Clones XC205 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 42% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000216517 (Chr9:44566644..44566849 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTTGGCGGATTTGGTAGTTC Chr9:44566731..44566750 59.94 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000216517 (Chr9:44566644..44566849 -)
Downstram Exon
ENSMUSE00000216518 (Chr9:44565203..44565367 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTTGGCGGATTTGGTAGTTC Chr9:44566731..44566750 59.94 45 TAGGTGGAGCATGCACTTTG Chr9:44565194..44565213 59.86 50

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
upstream ENSMUSE00000370160 Chr9:44568045..44568308 AAGCGGGAAAGGCTATTGTT Chr9:44568261..44568280 60.1 45
upstream ENSMUSE00000216521 Chr9:44566964..44567143 TATTGCCGAGCCTTAGAGGA Chr9:44567115..44567134 59.94 50
upstream ENSMUSE00000216517 Chr9:44566644..44566849 TTTGGCGGATTTGGTAGTTC Chr9:44566731..44566750 59.94 45

*** Putative Vector Insertion (Chr 9: 44565368 - 44566643) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 AGGATGCAGAGGAAGGCTTA Chr9:44566590..44566610 59.03 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector

Come back to gene ENSMUSG00000032096