Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2808
Trapped Gene
1110033M05Rik (ENSMUSG00000064138)
Vector Insertion
Chr 13: 77901200 - 77964583
Public Clones AG0505 (sanger) AG0492 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 36% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000327838 (Chr13:77901099..77901199 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACAGGTGGAACCAGAAAAGA Chr13:77901161..77901181 60.13 47.62 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000327838 (Chr13:77901099..77901199 +)
Downstram Exon
ENSMUSE00000453983 (Chr13:77964584..77964649 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACAGGTGGAACCAGAAAAGA Chr13:77901161..77901181 60.13 47.62 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000709178 Chr13:77847983..77848114 CGCGGATCTTGAGAGAGAAA Chr13:77847998..77848017 60.62 50
upstream ENSMUSE00000717096 Chr13:77847983..77848114 CGCGGATCTTGAGAGAGAAA Chr13:77847998..77848017 60.62 50
upstream ENSMUSE00000327844 Chr13:77898689..77898790 AAGGACGAACCACCTTTTGA Chr13:77898727..77898746 59.57 45
upstream ENSMUSE00000641045 Chr13:77898689..77898790 AAGGACGAACCACCTTTTGA Chr13:77898727..77898746 59.57 45
upstream ENSMUSE00000327838 Chr13:77901099..77901199 CACAGGTGGAACCAGAAAAGA Chr13:77901161..77901181 60.13 47.62

*** Putative Vector Insertion (Chr 13: 77901200 - 77964583) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000453983 Chr13:77964584..77964649 No primer for this exon
downstream ENSMUSE00000327822 Chr13:77973771..77973962 CTGCCCTGACAACACCACTA Chr13:77973885..77973904 59.74 55
downstream ENSMUSE00000563997 Chr13:77976493..77976552 GATTGCAGGGCCATCTACTT Chr13:77976549..77976568 59.15 50
downstream ENSMUSE00000501965 Chr13:78041915..78042136 TTTGAGGGTTGCGGTACTTC Chr13:78042107..78042126 60.11 50
downstream ENSMUSE00000496125 Chr13:78091246..78091365 CATAGACCGCATGCTCTTCA Chr13:78091282..78091301 59.97 50
downstream ENSMUSE00000476708 Chr13:78138847..78138963 AGTCTGTCAATGCCACAGCA Chr13:78138907..78138926 60.47 50
downstream ENSMUSE00000570078 Chr13:78145649..78145733 ACAGTCAGGCAGCATGGATT Chr13:78145720..78145739 60.69 50
downstream ENSMUSE00000641044 Chr13:78302774..78305491 CCCTGCATAGGTTTTTCCAA Chr13:78304683..78304702 59.93 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATTTAATCGCCTTGCAGCAC Chr13:77946247..77946268 60.24 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGGTATTCGTGACTGGGAAAA Chr13:77904244..77904265 60.35 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000064138