Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI38380
Trapped Gene
5033411D12Rik (ENSMUSG00000055137)
Vector Insertion
Chr 13: 17415038 - 17544387
Public Clones (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 62% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000447078 (Chr13:17544291..17544386 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGCATGTTTGACCCAAGTA Chr13:17544366..17544385 59.96 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000447078 (Chr13:17544291..17544386 -)
Downstram Exon
ENSMUSE00000325500 (Chr13:17415039..17415110 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGCATGTTTGACCCAAGTA Chr13:17544366..17544385 59.96 45 CTTGCATACCACAGCAAACTG Chr13:17415017..17415037 59.4 47.62

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000447092 Chr13:17786473..17786566 No primer for this exon
upstream ENSMUSE00000447061 Chr13:17764385..17764436 GACAGTATGAAGCCCCTGGA Chr13:17764412..17764431 60.07 55
upstream ENSMUSE00000447054 Chr13:17763535..17763608 TTGCCACGATGAATTTAGGA Chr13:17763572..17763591 59.11 40
upstream ENSMUSE00000447048 Chr13:17754573..17754658 GGGGACCTCCTTTTGTGAAC Chr13:17754615..17754634 60.72 55
upstream ENSMUSE00000447042 Chr13:17754053..17754103 TCAAGGATCCAAGAGGAGTGA Chr13:17754067..17754087 59.79 47.62
upstream ENSMUSE00000447037 Chr13:17736615..17736735 CTTGCAGCCATTTGTGATGT Chr13:17736716..17736735 59.72 45
upstream ENSMUSE00000447033 Chr13:17669324..17669415 No primer for this exon
upstream ENSMUSE00000447030 Chr13:17646160..17646303 ATTATGGCTGGCCTCCTACA Chr13:17646215..17646234 59.55 50
upstream ENSMUSE00000447078 Chr13:17544291..17544386 TGGCATGTTTGACCCAAGTA Chr13:17544366..17544385 59.96 45
upstream ENSMUSE00000325500 Chr13:17415039..17415110 No primer for this exon

*** Putative Vector Insertion (Chr 13: 17415038 - 17544387) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000361661 Chr13:17393752..17393849 CCCGAAGATGGTTCGTTCTA Chr13:17393770..17393789 60.07 50
downstream ENSMUSE00000469948 Chr13:17344325..17344427 CCTTCAGGCTGTTGATTGGT Chr13:17344323..17344342 60.11 50
downstream ENSMUSE00000520278 Chr13:17067991..17068054 TTCCCCACAGTTGGATGATT Chr13:17067983..17068002 60.17 45
downstream ENSMUSE00000618096 Chr13:16949689..16949852 TCTCAATAGCCCCCTCATCA Chr13:16949711..16949730 60.56 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTACCCACATCCCAACGTA Chr13:17445334..17445354 60.78 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TATGCTTGCTACCCACATCC Chr13:17445341..17445361 58.6 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000055137