Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1412
Trapped Gene
Srcap (ENSMUSG00000053877)
Vector Insertion
Chr 7: 134696809 - 134700921
Public Clones CH0649 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 68% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000587989 (Chr7:134696689..134696808 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GACCATCAGGGAACTGTTTGA Chr7:134696691..134696711 59.96 47.62 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000587989 (Chr7:134696689..134696808 +)
Downstram Exon
ENSMUSE00000587988 (Chr7:134700922..134701122 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GACCATCAGGGAACTGTTTGA Chr7:134696691..134696711 59.96 47.62 CTTCATCTTCTGCCCGACAT Chr7:134700949..134700968 60.22 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000632358 Chr7:134655516..134655852 GGTAGCGATAACGAGCCTTG Chr7:134655541..134655560 59.87 55
upstream ENSMUSE00000434975 Chr7:134657679..134657754 AGACTCTCACAGGGGGTGTG Chr7:134657719..134657738 60.15 60
upstream ENSMUSE00000708270 Chr7:134659456..134659715 GCAACGGTGATAACCCAGTC Chr7:134659603..134659622 60.38 55
upstream ENSMUSE00000715889 Chr7:134659456..134659715 GCAACGGTGATAACCCAGTC Chr7:134659603..134659622 60.38 55
upstream ENSMUSE00000705496 Chr7:134659662..134659715 CCTCAGCTCCCAATCCTACA Chr7:134659689..134659708 60.21 55
upstream ENSMUSE00000434971 Chr7:134663095..134663346 CAGATTCTAGTGGGGCAGGA Chr7:134663153..134663172 60.21 55
upstream ENSMUSE00000669344 Chr7:134663095..134663346 CAGATTCTAGTGGGGCAGGA Chr7:134663153..134663172 60.21 55
upstream ENSMUSE00000669352 Chr7:134663095..134663116 No primer for this exon
upstream ENSMUSE00000632356 Chr7:134663171..134663346 TTCCTCACTGGATGGACCTC Chr7:134663202..134663221 60.05 55
upstream ENSMUSE00000434965 Chr7:134664990..134665076 AACTTCGGAAGGAGGGATTC Chr7:134665018..134665037 59.51 50
upstream ENSMUSE00000588014 Chr7:134664990..134665175 ATTGCTGAACTTCGGAAGGA Chr7:134665011..134665030 59.81 45
upstream ENSMUSE00000434591 Chr7:134665081..134665175 CTTTGCTCAGGAACGCAGAT Chr7:134665133..134665152 60.54 50
upstream ENSMUSE00000632343 Chr7:134665503..134665518 No primer for this exon
upstream ENSMUSE00000632355 Chr7:134665503..134665643 CATGAAGAGCAGCGACAAAA Chr7:134665527..134665546 60.13 45
upstream ENSMUSE00000632354 Chr7:134668807..134669029 CGGTTTCTCGACTGGATGAT Chr7:134669006..134669025 60.07 50
upstream ENSMUSE00000632353 Chr7:134669145..134669419 AGGATGGGCCTGAAGAAAAT Chr7:134669370..134669389 59.9 45
upstream ENSMUSE00000632352 Chr7:134671910..134672003 TCTTCCGCTGTCACACAATG Chr7:134671922..134671941 60.87 50
upstream ENSMUSE00000588009 Chr7:134672649..134672738 GCTGAAGAGCAGTTGGAAGG Chr7:134672675..134672694 60.13 55
upstream ENSMUSE00000588023 Chr7:134672652..134672738 GCTGAAGAGCAGTTGGAAGG Chr7:134672675..134672694 60.13 55
upstream ENSMUSE00000632351 Chr7:134673697..134673873 CTATGCCTGTGATGCCTCTG Chr7:134673740..134673759 59.42 55
upstream ENSMUSE00000588007 Chr7:134673954..134674091 GGGAGTTCACAGTCGGAAGA Chr7:134674013..134674032 60.24 55
upstream ENSMUSE00000588021 Chr7:134673954..134674312 CCGGTCCTACGACCACTCTA Chr7:134674212..134674231 60.13 60
upstream ENSMUSE00000588006 Chr7:134674128..134674312 CCGGTCCTACGACCACTCTA Chr7:134674212..134674231 60.13 60
upstream ENSMUSE00000632350 Chr7:134674408..134674585 CCAGCTCCGAGAGTACCAAC Chr7:134674440..134674459 59.87 60
upstream ENSMUSE00000632349 Chr7:134674849..134674985 ACCAGCGTGATGTTGAATTG Chr7:134674881..134674900 59.57 45
upstream ENSMUSE00000632348 Chr7:134675234..134675403 ACCAGGCTTTTCGTCGTAAG Chr7:134675298..134675317 59.38 50
upstream ENSMUSE00000632347 Chr7:134675541..134675733 GGTCTAGTCAAACGCCTCCA Chr7:134675710..134675729 60.26 55
upstream ENSMUSE00000632346 Chr7:134678062..134678198 GCCGAGTTAAGGTGGATGTT Chr7:134678084..134678103 59.06 50
upstream ENSMUSE00000588000 Chr7:134678289..134678475 TTGACCCTCGACCTGTTACC Chr7:134678378..134678397 59.97 55
upstream ENSMUSE00000632345 Chr7:134678289..134678493 TTGACCCTCGACCTGTTACC Chr7:134678378..134678397 59.97 55
upstream ENSMUSE00000587999 Chr7:134681515..134681684 GACATGGGTCGGTTTGATCT Chr7:134681521..134681540 59.79 50
upstream ENSMUSE00000587998 Chr7:134682017..134682282 AAGAAGGCCGTACAGTGGTG Chr7:134682040..134682059 60.17 55
upstream ENSMUSE00000587997 Chr7:134683271..134683435 ATCCAGGGCAACAAACTGAC Chr7:134683360..134683379 59.97 50
upstream ENSMUSE00000587996 Chr7:134684170..134684436 GCCCTACGTTAACCCCTAGC Chr7:134684311..134684330 59.99 60
upstream ENSMUSE00000587995 Chr7:134684756..134686221 GACACTGACTCTGCGCTCTG Chr7:134686110..134686129 59.92 60
upstream ENSMUSE00000587994 Chr7:134692654..134692919 TGGATCGGATTTTCCAACTT Chr7:134692697..134692716 59.36 40
upstream ENSMUSE00000587993 Chr7:134693047..134693249 TCTTTGTCATGCCTCCTGTG Chr7:134693052..134693071 59.83 50
upstream ENSMUSE00000587992 Chr7:134695773..134695942 GGCCATCTGTATTTGCGTCT Chr7:134695892..134695911 60.1 50
upstream ENSMUSE00000587991 Chr7:134696082..134696278 AATTGGTCAAACTCGGGATG Chr7:134696246..134696265 59.79 45
upstream ENSMUSE00000587990 Chr7:134696376..134696490 TTGGGAGATATGGCCATTGA Chr7:134696437..134696456 61.2 45
upstream ENSMUSE00000587989 Chr7:134696689..134696808 GACCATCAGGGAACTGTTTGA Chr7:134696691..134696711 59.96 47.62

*** Putative Vector Insertion (Chr 7: 134696809 - 134700921) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000587988 Chr7:134700922..134701122 CTTCATCTTCTGCCCGACAT Chr7:134700949..134700968 60.22 50
downstream ENSMUSE00000587987 Chr7:134701280..134701363 TTCTGCCTGTTTGAGCTCCT Chr7:134701366..134701385 60.13 50
downstream ENSMUSE00000527011 Chr7:134701482..134701821 AGTCGGAACACCTCCTCCTT Chr7:134701543..134701562 60.11 55
downstream ENSMUSE00000587986 Chr7:134701963..134704280 CTTCTTGGACTGGCGCTAAC Chr7:134702974..134702993 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGATGAAGAGGAGGCTGTGG Chr7:134699761..134699781 59.4 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTTCGTGACTGGGAAAACC Chr7:134699856..134699876 60.93 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000053877