Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8225
Trapped Gene
AC165281.2 (ENSMUSG00000042590)
Vector Insertion
Chr 13: 107715237 - 107726839
Public Clones (sanger) RRF204 (baygenomics) E043E01 (ggtc) P024F11 (ggtc) P062C12 (ggtc)
(ggtc) PST21532-NR (escells) PST17540-NR (escells) PST24756-NR (escells)
IST11616D5 (tigm) IST14663E6 (tigm) IST14547B7 (tigm) IST14114F4 (tigm)
IST14999G8 (tigm) IST14134G7 (tigm) IST10548H1 (tigm) IST10984H11 (tigm)
IST14886C12 (tigm) IST14162E3 (tigm) IST14253E1 (tigm)
Private Clones OST377664 (lexicon) OST302718 (lexicon) OST299318 (lexicon) OST225823 (lexicon)
OST221714 (lexicon) OST212343 (lexicon) OST164829 (lexicon) OST116307 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000508911 (Chr13:107726840..107726995 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCGTTCCTAGAAGCCGTTTT Chr13:107726959..107726978 60.74 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000508911 (Chr13:107726840..107726995 -)
Downstram Exon
ENSMUSE00000610475 (Chr13:107715093..107715236 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCGTTCCTAGAAGCCGTTTT Chr13:107726959..107726978 60.74 50 TGACTGGTGGCCTGTGTTAG Chr13:107715150..107715169 59.74 55

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

*** Putative Vector Insertion (Chr 13: 107715237 - 107726839) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000610475 Chr13:107715093..107715236 TGACTGGTGGCCTGTGTTAG Chr13:107715150..107715169 59.74 55
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 GGTTCACTTGCTTGCTCTTTG Chr13:107720831..107720852 60.04 47.62 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTTCACTTGCTTGCTCTTTG Chr13:107720831..107720852 60.04 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCTTCCACTAATCCCCTTCC Chr13:107720987..107721007 59.76 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GTAGCGTGACTGGGAAAACC Chr13:107720929..107720949 59.6 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042590