Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI23647
Trapped Gene
Ncapd2 (ENSMUSG00000038252)
Vector Insertion
Chr 6: 125139927 - 125141515
Public Clones (ggtc) E052D03 (ggtc) (ggtc) IST12256A8 (tigm)
Private Clones OST250621 (lexicon) OST152362 (lexicon) OST148940 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000341330 (Chr6:125141516..125141613 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCGTATCCTGCCCTATTGTT Chr6:125141587..125141606 59.07 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000341330 (Chr6:125141516..125141613 -)
Downstram Exon
ENSMUSE00000401504 (Chr6:125139781..125139926 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCGTATCCTGCCCTATTGTT Chr6:125141587..125141606 59.07 50 CTCCCGGACAACGTACTGAT Chr6:125139796..125139815 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000341330 Chr6:125141516..125141613 GCGTATCCTGCCCTATTGTT Chr6:125141587..125141606 59.07 50

*** Putative Vector Insertion (Chr 6: 125139927 - 125141515) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000401504 Chr6:125139781..125139926 CTCCCGGACAACGTACTGAT Chr6:125139796..125139815 59.99 55
downstream ENSMUSE00000243668 Chr6:125137095..125137170 CTCGGAAGGCAGACTGAAAT Chr6:125137128..125137147 59.43 50
downstream ENSMUSE00000243660 Chr6:125136772..125136830 GTCTTCCTTGAGGCCAGGTT Chr6:125136772..125136791 60.63 55
downstream ENSMUSE00000243656 Chr6:125136118..125136299 GGACTCCAAAAGGCGTATCA Chr6:125136150..125136169 60.07 50
downstream ENSMUSE00000243650 Chr6:125135712..125135854 GCTGGAGCAGCTGTGTTAAA Chr6:125135742..125135761 59.22 50
downstream ENSMUSE00000243641 Chr6:125134453..125134580 CATATGGTTGTAGCGGACCA Chr6:125134435..125134454 59.42 50
downstream ENSMUSE00000337778 Chr6:125134247..125134370 CACAGACTCACGGCTGTCAC Chr6:125134270..125134289 60.53 60
downstream ENSMUSE00000243905 Chr6:125133932..125134079 TCCATCCAGATGGTCTAGCA Chr6:125133913..125133932 59.19 50
downstream ENSMUSE00000243897 Chr6:125130997..125131194 CTAACACAGCATTGCGCATC Chr6:125131145..125131164 60.43 50
downstream ENSMUSE00000243889 Chr6:125129713..125129847 AGCAGCTGAATGGCATTTTT Chr6:125129728..125129747 59.85 40
downstream ENSMUSE00000243881 Chr6:125129531..125129618 AGTGGTCCAGCAAGGTCAAT Chr6:125129568..125129587 59.58 50
downstream ENSMUSE00000243873 Chr6:125129256..125129430 GCAGGGTCGACTTCAATTCT Chr6:125129346..125129365 59.29 50
downstream ENSMUSE00000243864 Chr6:125127827..125127942 CTGGTAGCTTCCCGAGTGAG Chr6:125127888..125127907 60.01 60
downstream ENSMUSE00000243856 Chr6:125127346..125127570 TCCTGCAGATACTGCACCAG Chr6:125127401..125127420 60.01 55
downstream ENSMUSE00000243850 Chr6:125126670..125126844 TCGGGTTGAGGTAGAGTTGG Chr6:125126664..125126683 60.1 55
downstream ENSMUSE00000243843 Chr6:125126161..125126245 CAACAGCGAGAGGTTGTGAA Chr6:125126184..125126203 60.03 50
downstream ENSMUSE00000243838 Chr6:125124243..125124376 CCATCATGCCAAGAAGCATA Chr6:125124225..125124244 59.65 45
downstream ENSMUSE00000243831 Chr6:125123798..125123930 TTCCTCCTGTCCGAGATGTT Chr6:125123777..125123796 59.65 50
downstream ENSMUSE00000243826 Chr6:125123619..125123703 TCCTGAAGTCGCTCAAACAA Chr6:125123611..125123630 59.57 45
downstream ENSMUSE00000243820 Chr6:125123378..125123542 CTTTGAATGGGATCCAGAGG Chr6:125123482..125123501 59.48 50
downstream ENSMUSE00000243815 Chr6:125123008..125123180 CCACTCACTGCTTGTTCCAA Chr6:125123053..125123072 59.87 50
downstream ENSMUSE00000243811 Chr6:125121851..125121965 TCACAGATGCTTCGGATGAG Chr6:125121846..125121865 59.94 50
downstream ENSMUSE00000243807 Chr6:125121654..125121777 TTGCTGTATAAGCCAGGGTTG Chr6:125121686..125121706 60.14 47.62
downstream ENSMUSE00000243800 Chr6:125121416..125121571 AGGTTAGGGAAGCGGATAGC Chr6:125121427..125121446 59.71 55
downstream ENSMUSE00000243794 Chr6:125120934..125121111 TGTCTTCCGCACTTGTTGAG Chr6:125121056..125121075 60.03 50
downstream ENSMUSE00000243787 Chr6:125120745..125120839 TCTGACAGGCGACTGATGAT Chr6:125120768..125120787 59.37 50
downstream ENSMUSE00000243779 Chr6:125120152..125120232 ACCGCTGACACAGCTTTTCT Chr6:125120143..125120162 60.06 50
downstream ENSMUSE00000243771 Chr6:125119833..125120016 ATCGCCAAAGCACTCAAAGT Chr6:125119892..125119911 59.88 45
downstream ENSMUSE00000243761 Chr6:125118881..125119007 ATCCATGCCTCTGGTGTGAC Chr6:125118929..125118948 60.97 55
downstream ENSMUSE00000243752 Chr6:125118608..125118766 ACGACCAGGTTTGGTACGTC Chr6:125118662..125118681 59.89 55
downstream ENSMUSE00000691073 Chr6:125118287..125118337 GGGTGGTTCTCTTGGGTGTC Chr6:125118268..125118287 61.75 60
downstream ENSMUSE00000691072 Chr6:125118106..125118176 GGCCATTTCCATGTTAAAACC Chr6:125118108..125118128 60.41 42.86
downstream ENSMUSE00000385544 Chr6:125118027..125118337 GAAAACAGCAATTGGCACAG Chr6:125118033..125118052 59.32 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAAAAAGCTAATCGCCTTGC Chr6:125141452..125141472 59.1 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTTGAGAAAAAGCCGTGAC Chr6:125141458..125141478 59.72 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCGCTAGCTTGAAAACCATC Chr6:125141617..125141637 59.85 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCGCTAGCTTGAAAACCATC Chr6:125141617..125141637 59.85 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000038252