Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9083
Trapped Gene
Atp7a (ENSMUSG00000033792)
Vector Insertion
Chr X: 103265108 - 103265247
Public Clones XK122 (baygenomics) XK523 (baygenomics)
Private Clones OST420063 (lexicon) OST376981 (lexicon) OST338203 (lexicon) OST308160 (lexicon)
OST265952 (lexicon) OST220676 (lexicon) OST210051 (lexicon) OST187449 (lexicon)
OST169552 (lexicon) OST168362 (lexicon) OST138372 (lexicon) OST118451 (lexicon)
OST114384 (lexicon) OST77493 (lexicon) OST64192 (lexicon) OST58774 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000718084 (ChrX:103265109..103265246 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAATGGAGCCAAGTGTGGAT ChrX:103265125..103265144 59.41 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000718084 (ChrX:103265109..103265246 +)
Downstram Exon
ENSMUSE00000281475 (ChrX:103265109..103265246 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAATGGAGCCAAGTGTGGAT ChrX:103265125..103265144 59.41 45 TCCCAATCTGCTGTTCAATG ChrX:103265223..103265242 59.65 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000696136 ChrX:103222615..103222718 No primer for this exon
upstream ENSMUSE00000333467 ChrX:103222656..103222718 No primer for this exon

*** Putative Vector Insertion (Chr X: 103265108 - 103265247) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000281475 ChrX:103265109..103265246 TCCCAATCTGCTGTTCAATG ChrX:103265223..103265242 59.65 45
downstream ENSMUSE00000718084 ChrX:103265109..103265246 TCCCAATCTGCTGTTCAATG ChrX:103265223..103265242 59.65 45
downstream ENSMUSE00000378424 ChrX:103280453..103280942 TTAATGCGCTGAACACCTTG ChrX:103280943..103280962 59.87 45
downstream ENSMUSE00000281456 ChrX:103281428..103282153 AGAGCTGGCGGTACTTTCAA ChrX:103281891..103281910 60.01 50
downstream ENSMUSE00000696147 ChrX:103283674..103283856 AGGGCAAAAGAGGTGTTTCC ChrX:103283739..103283758 60.48 50
downstream ENSMUSE00000337195 ChrX:103283677..103283856 AAGCACAGGTCATCCCAGAG ChrX:103283817..103283836 60.26 55
downstream ENSMUSE00000281433 ChrX:103287423..103287586 CACTCGGGGTTGGATAACAG ChrX:103287505..103287524 60.37 55
downstream ENSMUSE00000281421 ChrX:103290192..103290353 GGAAGCACACGTCATTCCTC ChrX:103290218..103290237 60.67 55
downstream ENSMUSE00000281413 ChrX:103292116..103292192 No primer for this exon
downstream ENSMUSE00000378036 ChrX:103292729..103292954 AGGATCTGACGCTCCAGAAA ChrX:103292902..103292921 59.95 50
downstream ENSMUSE00000386154 ChrX:103294125..103294358 GAGTAGGCAAATGCGATGGT ChrX:103294237..103294256 60.1 50
downstream ENSMUSE00000281384 ChrX:103295866..103295957 No primer for this exon
downstream ENSMUSE00000281379 ChrX:103297199..103297326 GGGACTCGTCCACCATAGAA ChrX:103297320..103297339 59.93 55
downstream ENSMUSE00000281373 ChrX:103297686..103297840 TTGCTCGGATGAGGAGAGAT ChrX:103297775..103297794 59.91 50
downstream ENSMUSE00000281369 ChrX:103298051..103298185 GCCACTGAGTTTGTCTGCAA ChrX:103298089..103298108 60.03 50
downstream ENSMUSE00000281362 ChrX:103300486..103300680 ACAGGGACATGCGATACACA ChrX:103300578..103300597 59.99 50
downstream ENSMUSE00000281357 ChrX:103302523..103302705 TACTTTCTGCAGTCCCCACA ChrX:103302661..103302680 59.29 50
downstream ENSMUSE00000281350 ChrX:103305100..103305316 No primer for this exon
downstream ENSMUSE00000281343 ChrX:103310429..103310575 ATCCATTCCCGGTTACCAAT ChrX:103310483..103310502 60.26 45
downstream ENSMUSE00000281335 ChrX:103313591..103313733 GCAATAGCAATCAAGCCACA ChrX:103313621..103313640 59.84 45
downstream ENSMUSE00000281327 ChrX:103315574..103315777 CAGCTGCTTCAATGGCTACA ChrX:103315763..103315782 60.16 50
downstream ENSMUSE00000394198 ChrX:103316929..103317046 ACTTGCCACAACATCCAGAA ChrX:103316958..103316977 59.14 45
downstream ENSMUSE00000281307 ChrX:103318682..103318784 GATCCCATCCAGGGTTGTAA ChrX:103318730..103318749 59.6 50
downstream ENSMUSE00000281295 ChrX:103319678..103320069 CAGAAGCGAGTGCTTGTCAG ChrX:103319918..103319937 59.92 55
downstream ENSMUSE00000696135 ChrX:103319678..103320256 CAGAAGCGAGTGCTTGTCAG ChrX:103319918..103319937 59.92 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGCCAAGTGTGGATGCAAAT ChrX:103265132..103265152 60.53 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGCCAAGTGTGGATGCAAAT ChrX:103265132..103265152 60.53 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000033792