Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI7597
Trapped Gene
AC165281.2 (ENSMUSG00000042590)
Vector Insertion
Chr 13: 107709705 - 107715092
Public Clones RRR432 (baygenomics) (egtc) IST11566D3 (tigm) IST14524C10 (tigm) IST14617B4 (tigm)
Private Clones OST383152 (lexicon) OST224927 (lexicon) OST223635 (lexicon) OST220001 (lexicon)
OST200278 (lexicon)
Severity of mutation (?) Insertion after 5% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000610475 (Chr13:107715093..107715236 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTAACACAGGCCACCAGTCA Chr13:107715172..107715191 59.74 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000610475 (Chr13:107715093..107715236 -)
Downstram Exon
ENSMUSE00000610474 (Chr13:107709604..107709704 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTAACACAGGCCACCAGTCA Chr13:107715172..107715191 59.74 55 CGCCTCCAGTAACGATCAAT Chr13:107709594..107709613 60.1 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000508911 Chr13:107726840..107726995 GCGTTCCTAGAAGCCGTTTT Chr13:107726959..107726978 60.74 50
upstream ENSMUSE00000610475 Chr13:107715093..107715236 CTAACACAGGCCACCAGTCA Chr13:107715172..107715191 59.74 55

*** Putative Vector Insertion (Chr 13: 107709705 - 107715092) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000610474 Chr13:107709604..107709704 CGCCTCCAGTAACGATCAAT Chr13:107709594..107709613 60.1 50
downstream ENSMUSE00000610473 Chr13:107700824..107700896 TGCACGCAATGTTGACTTTT Chr13:107700838..107700857 60.3 40
downstream ENSMUSE00000610472 Chr13:107700280..107700483 GTCTAACCGAGCAACCTTGG Chr13:107700414..107700433 59.73 55
downstream ENSMUSE00000610471 Chr13:107690765..107690897 ATTGCCAGAAGAAACGTGCT Chr13:107690792..107690811 59.88 45
downstream ENSMUSE00000610470 Chr13:107688999..107689057 CACAGTTAACTTCCGCAGCA Chr13:107689016..107689035 60.05 50
downstream ENSMUSE00000610469 Chr13:107687296..107687344 No primer for this exon
downstream ENSMUSE00000610468 Chr13:107685885..107685955 No primer for this exon
downstream ENSMUSE00000610467 Chr13:107682503..107682695 TGGACAATGAATCGCTCAAA Chr13:107682546..107682565 60.2 40
downstream ENSMUSE00000610466 Chr13:107681696..107681848 CCTCCCACATGGTCAGTTCT Chr13:107681692..107681711 59.96 55
downstream ENSMUSE00000610465 Chr13:107679443..107679486 No primer for this exon
downstream ENSMUSE00000610464 Chr13:107676747..107676837 No primer for this exon
downstream ENSMUSE00000610463 Chr13:107673606..107673653 No primer for this exon
downstream ENSMUSE00000334627 Chr13:107672922..107673027 AGCAGCTAATCCCACAGCAT Chr13:107672980..107672999 59.87 50
downstream ENSMUSE00000393320 Chr13:107669693..107669819 CCTGCGTCGTAATGGCTTAT Chr13:107669776..107669795 60.12 50
downstream ENSMUSE00000568985 Chr13:107667015..107667048 No primer for this exon
downstream ENSMUSE00000639865 Chr13:107666319..107666359 No primer for this exon
downstream ENSMUSE00000610461 Chr13:107665571..107665687 TGCACGTTGACTCTTTCGAT Chr13:107665550..107665569 59.44 45
downstream ENSMUSE00000610460 Chr13:107660755..107660868 GTGTTCTTCGCTCTGCTTCC Chr13:107660781..107660800 60.14 55
downstream ENSMUSE00000610459 Chr13:107655945..107656060 CTGGATAACTGGGAGCAGGA Chr13:107655985..107656004 60.21 55
downstream ENSMUSE00000311873 Chr13:107650941..107651017 ATGGGCTGTTCTCCAATGTC Chr13:107650970..107650989 59.93 50
downstream ENSMUSE00000679785 Chr13:107647579..107647605 No primer for this exon
downstream ENSMUSE00000311865 Chr13:107647309..107647388 GCCATTGATGATCTTAAAGCAG Chr13:107647320..107647341 58.86 40.91
downstream ENSMUSE00000339319 Chr13:107646818..107646898 AAAGGACTGGCACAAACCTG Chr13:107646847..107646866 60.15 50
downstream ENSMUSE00000382317 Chr13:107638321..107638416 TGAAACATCTGTGGGCCTAA Chr13:107638342..107638361 59.12 45
downstream ENSMUSE00000405267 Chr13:107637426..107637539 AAGACTCGACCCATGACAGC Chr13:107637468..107637487 60.27 55
downstream ENSMUSE00000504867 Chr13:107632169..107632290 TTCTTTCTTTCGGGCTGTGT Chr13:107632192..107632211 59.85 45
downstream ENSMUSE00000610458 Chr13:107626292..107626476 TCTGCAGAGCTCCGTTCTTT Chr13:107626320..107626339 60.28 50
downstream ENSMUSE00000311949 Chr13:107613036..107613131 GACATCATGAAGAGCCTCCAC Chr13:107613049..107613069 59.68 52.38
downstream ENSMUSE00000311942 Chr13:107602288..107602372 ACTTTCGGTTCCTCGTGTTG Chr13:107602315..107602334 60.15 50
downstream ENSMUSE00000679784 Chr13:107585711..107585875 TTTCCATGAGGGACTGGAAG Chr13:107585742..107585761 60.04 50
downstream ENSMUSE00000311936 Chr13:107584520..107585875 GGTTCCTCACAATGGCAAGT Chr13:107584694..107584713 59.97 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCAGCTGAAACAGTGGGAGA Chr13:107712120..107712140 61.55 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCAGCTGAAACAGTGGGAGA Chr13:107712120..107712140 61.55 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TAATAATCGCCTTGCAGCAC Chr13:107712169..107712189 58.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TCCGCCATCATTCTCTCTCT Chr13:107712243..107712263 59.91 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042590