Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14525
Trapped Gene
Rbm16 (ENSMUSG00000046201)
Vector Insertion
Chr 17: 3150944 - 3159162
Public Clones (sanger) (sanger) (sanger) (sanger) (sanger) (sanger)
(sanger) D077H08 (ggtc) D076H09 (ggtc) (ggtc) D153F04 (ggtc)
D077E07 (ggtc) E076D06 (ggtc) D076G09 (ggtc) D153F04 (ggtc) D076H09 (ggtc)
(ggtc) E076D06 (ggtc) D076G09 (ggtc) CMHD-GT_536C4-5S (cmhd) FHCRC-GT-S7-6E1 (fhcrc)
IST14849D3 (tigm) IST14794D2 (tigm) IST14879E5 (tigm)
Private Clones OST30163 (lexicon)
Severity of mutation (?) Insertion after 4% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000547043 (Chr17:3150785..3150943 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CATGTGGTTGCTGGAATTTG Chr17:3150880..3150899 59.96 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000547043 (Chr17:3150785..3150943 +)
Downstram Exon
ENSMUSE00000379333 (Chr17:3159163..3159324 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CATGTGGTTGCTGGAATTTG Chr17:3150880..3150899 59.96 45 ATTGTCGCACAATGGAGTCA Chr17:3159223..3159242 60.12 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000658492 Chr17:3114967..3115418 GTGGGAGGAAGAGGAAGGAG Chr17:3115070..3115089 60.19 60
upstream ENSMUSE00000658491 Chr17:3114979..3115418 GTGGGAGGAAGAGGAAGGAG Chr17:3115070..3115089 60.19 60
upstream ENSMUSE00000367004 Chr17:3145075..3145158 AAAGGCAGCCATCAAAGCTA Chr17:3145134..3145153 59.98 45
upstream ENSMUSE00000468506 Chr17:3148536..3148580 No primer for this exon
upstream ENSMUSE00000547043 Chr17:3150785..3150943 CATGTGGTTGCTGGAATTTG Chr17:3150880..3150899 59.96 45

*** Putative Vector Insertion (Chr 17: 3150944 - 3159162) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000379333 Chr17:3159163..3159324 ATTGTCGCACAATGGAGTCA Chr17:3159223..3159242 60.12 45
downstream ENSMUSE00000345755 Chr17:3162959..3163112 CCAAAACAGGCGTGACAACT Chr17:3163082..3163101 61.12 50
downstream ENSMUSE00000392504 Chr17:3164147..3164277 TCAGGTAAGCCTTGGACCAC Chr17:3164201..3164220 60.11 55
downstream ENSMUSE00000348840 Chr17:3167963..3168139 CAAGGCCTGCAGGATAGAAG Chr17:3168034..3168053 59.97 55
downstream ENSMUSE00000333169 Chr17:3169327..3169406 TGCTCAGAATCTTCCCCAAA Chr17:3169370..3169389 60.71 45
downstream ENSMUSE00000445526 Chr17:3171103..3171220 GTCGCAACTGCTCCAAGTTC Chr17:3171191..3171210 60.99 55
downstream ENSMUSE00000367371 Chr17:3177093..3177224 TTGGCTACTCCCTTGTGAGG Chr17:3177170..3177189 60.25 55
downstream ENSMUSE00000280233 Chr17:3177611..3177723 CAACAACATCTTGCCCTTCA Chr17:3177647..3177666 59.69 45
downstream ENSMUSE00000280209 Chr17:3178155..3178348 CTTCCTGTGCTTTCGCTTTC Chr17:3178218..3178237 60.13 50
downstream ENSMUSE00000280184 Chr17:3185064..3185164 CTTGGCCAACCCAGAGAGTA Chr17:3185096..3185115 60.25 55
downstream ENSMUSE00000235905 Chr17:3185761..3185874 TTTCTGAAGAGCCCGAAATG Chr17:3185835..3185854 60.32 45
downstream ENSMUSE00000280138 Chr17:3187589..3187745 TATGTGACGCCAAGATCCAC Chr17:3187665..3187684 59.53 50
downstream ENSMUSE00000403192 Chr17:3190147..3190280 AGGAGGAGGGAAAACCTCTG Chr17:3190268..3190287 59.67 55
downstream ENSMUSE00000280487 Chr17:3191817..3191961 GGAAACGCTGGAGGAACTAA Chr17:3191872..3191891 59.31 50
downstream ENSMUSE00000445485 Chr17:3193014..3193082 TGGTACTACCGGTGGGATTG Chr17:3193081..3193100 60.63 55
downstream ENSMUSE00000280452 Chr17:3195778..3195993 GTCATGGACAATGGTGGTTG Chr17:3195808..3195827 59.66 50
downstream ENSMUSE00000400161 Chr17:3196760..3198855 GTAAGCCTTTTGGACCACCA Chr17:3197746..3197765 59.97 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTTTAATCGCCTTGCAGCAC Chr17:3150992..3151012 61.26 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTTTCGTGACTGGGAAAACC Chr17:3150991..3151011 59.57 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000046201