Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI30397
Trapped Gene
5830415L20Rik (ENSMUSG00000058503)
Vector Insertion
Chr 5: 3565751 - 3568986
Public Clones CMHD-GT_401C6-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000405213 (Chr5:3565703..3565750 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAGAAAAGCGGTGAAGAGC Chr5:3565717..3565736 59.2 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000405213 (Chr5:3565703..3565750 +)
Downstram Exon
ENSMUSE00000703257 (Chr5:3568987..3569810 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAGAAAAGCGGTGAAGAGC Chr5:3565717..3565736 59.2 50 CAGAGTCACCAAGCACTGGA Chr5:3569285..3569304 60.02 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000656308 Chr5:3543833..3543947 No primer for this exon
upstream ENSMUSE00000703270 Chr5:3554316..3554335 No primer for this exon
upstream ENSMUSE00000703269 Chr5:3554638..3554736 CAATAGCAATGGCTCGATCA Chr5:3554652..3554671 59.79 45
upstream ENSMUSE00000184905 Chr5:3554639..3554736 CAATAGCAATGGCTCGATCA Chr5:3554652..3554671 59.79 45
upstream ENSMUSE00000184909 Chr5:3557744..3557822 AGGCTTTGGCTGAGTTTGAA Chr5:3557788..3557807 59.99 45
upstream ENSMUSE00000184908 Chr5:3558473..3558547 GGAAATGAGAGCTCATCCAAA Chr5:3558518..3558538 59.26 42.86
upstream ENSMUSE00000496161 Chr5:3558661..3558693 No primer for this exon
upstream ENSMUSE00000497715 Chr5:3559097..3559159 No primer for this exon
upstream ENSMUSE00000720344 Chr5:3559606..3559698 AAGAAGAGCCGTTGCCATAA Chr5:3559636..3559655 59.85 45
upstream ENSMUSE00000721940 Chr5:3559606..3559698 AAGAAGAGCCGTTGCCATAA Chr5:3559636..3559655 59.85 45
upstream ENSMUSE00000405924 Chr5:3561039..3561089 No primer for this exon
upstream ENSMUSE00000703264 Chr5:3561039..3561089 No primer for this exon
upstream ENSMUSE00000365015 Chr5:3564241..3564327 TCTGAGTCGCTGTCAGAGTCA Chr5:3564295..3564315 59.91 52.38
upstream ENSMUSE00000703262 Chr5:3564241..3564327 TCTGAGTCGCTGTCAGAGTCA Chr5:3564295..3564315 59.91 52.38
upstream ENSMUSE00000405213 Chr5:3565703..3565750 GAAGAAAAGCGGTGAAGAGC Chr5:3565717..3565736 59.2 50
upstream ENSMUSE00000703260 Chr5:3565703..3565750 GAAGAAAAGCGGTGAAGAGC Chr5:3565717..3565736 59.2 50

*** Putative Vector Insertion (Chr 5: 3565751 - 3568986) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000656303 Chr5:3568987..3570548 CAGAGTCACCAAGCACTGGA Chr5:3569285..3569304 60.02 55
downstream ENSMUSE00000703257 Chr5:3568987..3569810 CAGAGTCACCAAGCACTGGA Chr5:3569285..3569304 60.02 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCGTGAGAGAACAACAGCAA Chr5:3565736..3565756 60.18 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCGTGAGAGAACAACAGCAA Chr5:3565736..3565756 60.18 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000058503