Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8089
Trapped Gene
Slc38a9 (ENSMUSG00000047789)
Vector Insertion
Chr 13: 113459940 - 113476273
Public Clones RRF540 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 7% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000354921 (Chr13:113459795..113459939 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGGCCTATGAACATCCAGT Chr13:113459892..113459911 60.34 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000354921 (Chr13:113459795..113459939 +)
Downstram Exon
ENSMUSE00000365765 (Chr13:113476274..113476406 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGGCCTATGAACATCCAGT Chr13:113459892..113459911 60.34 50 TTGTCTGCAGGAGTGGTGAG Chr13:113476402..113476421 60.02 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000435670 Chr13:113450984..113451080 TTTCCGACGTAGAGGGATTG Chr13:113451051..113451070 60.07 50
upstream ENSMUSE00000354921 Chr13:113459795..113459939 TGGGCCTATGAACATCCAGT Chr13:113459892..113459911 60.34 50

*** Putative Vector Insertion (Chr 13: 113459940 - 113476273) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000365765 Chr13:113476274..113476406 TTGTCTGCAGGAGTGGTGAG Chr13:113476402..113476421 60.02 55
downstream ENSMUSE00000408687 Chr13:113479481..113479602 TATAGGCAGAGCCCAATGGA Chr13:113479553..113479572 60.56 50
downstream ENSMUSE00000378819 Chr13:113479730..113479793 TGTTTTATGCCCCAAGGAAT Chr13:113479795..113479814 59.27 40
downstream ENSMUSE00000338903 Chr13:113480367..113480460 CGTACTCCGTGACTTCACCA Chr13:113480459..113480478 59.74 55
downstream ENSMUSE00000392484 Chr13:113485449..113485619 AATGAGCGACACCAAGGAGA Chr13:113485555..113485574 60.8 50
downstream ENSMUSE00000352033 Chr13:113488193..113488252 CAGGGTTGCTATTATTGGTGCT Chr13:113488253..113488274 60.38 45.46
downstream ENSMUSE00000349625 Chr13:113491665..113491859 GCCAGCATTTGGACATATCA Chr13:113491687..113491706 59.5 45
downstream ENSMUSE00000403016 Chr13:113493746..113493853 GCCTTCAGGGTAACAACGAA Chr13:113493794..113493813 60.11 50
downstream ENSMUSE00000342084 Chr13:113504349..113504455 AGAGTAAGCACCCCCATCAG Chr13:113504394..113504413 59.16 55
downstream ENSMUSE00000353578 Chr13:113513406..113513519 GTAATGGAGGCGAAGGGAAT Chr13:113513502..113513521 60.29 50
downstream ENSMUSE00000332822 Chr13:113516255..113516403 GTCACTGCTGGGGAAGTTGT Chr13:113516287..113516306 60.16 55
downstream ENSMUSE00000375637 Chr13:113519406..113519495 GTCACTCCAGCTCCCACAAT Chr13:113519459..113519478 60.12 55
downstream ENSMUSE00000467709 Chr13:113521707..113523106 GGGAATGAGGGTCACTGAGA Chr13:113522086..113522105 60.05 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AACCACTAATCGCCTTGCAG Chr13:113465985..113466005 60.27 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGGGCCTATGAACATCCAG Chr13:113465892..113465912 60.47 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000047789