Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI35611
Trapped Gene
Usp9y (ENSMUSG00000069044)
Vector Insertion
Chr Y: 646952 - 650301
Public Clones IST14870D3 (tigm) IST14488E2 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 86% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000568516 (ChrY:650171..650300 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CATGGGCGACATTTACAACA ChrY:650206..650225 60.38 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000568516 (ChrY:650171..650300 -)
Downstram Exon
ENSMUSE00000568513 (ChrY:646953..647138 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CATGGGCGACATTTACAACA ChrY:650206..650225 60.38 45 CCTGGTCCTTCATCCAAAGA ChrY:647038..647057 60.04 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000647292 ChrY:795966..796225 CTTTCCTTCACGTTGGTGGT ChrY:796109..796128 60.01 50
upstream ENSMUSE00000647291 ChrY:795329..795363 No primer for this exon
upstream ENSMUSE00000647290 ChrY:791051..791127 CCTGTGAGGAATCCAGAGTTG ChrY:791079..791099 59.71 52.38
upstream ENSMUSE00000557453 ChrY:790613..790754 ATCACAACTCGTGGCTCTCC ChrY:790683..790702 60.27 55
upstream ENSMUSE00000626493 ChrY:785294..785439 CCATATGAACAAGGCCAAGG ChrY:785375..785394 60.32 50
upstream ENSMUSE00000626492 ChrY:783273..783352 TGTTTTGCCAAAGGGAGAAT ChrY:783315..783334 59.55 40
upstream ENSMUSE00000626491 ChrY:780946..781058 AGGCTGTGAGTGGATGGAAG ChrY:780958..780977 60.26 55
upstream ENSMUSE00000626490 ChrY:778828..779046 GCACGTCCATGTGAATCAGT ChrY:778895..778914 59.56 50
upstream ENSMUSE00000626489 ChrY:771702..771817 CCAGATTTTGCATGATCGTTT ChrY:771750..771770 59.95 38.1
upstream ENSMUSE00000626488 ChrY:771249..771500 CCGTTTGGACAGTGCTATGA ChrY:771480..771499 59.72 50
upstream ENSMUSE00000626487 ChrY:770746..770881 TAACCGTTGAGCGAATGACA ChrY:770746..770765 60.26 45
upstream ENSMUSE00000626486 ChrY:768616..768768 No primer for this exon
upstream ENSMUSE00000626485 ChrY:748861..748965 TTGGCTTGGAATTTTTCTCC ChrY:748895..748914 59.13 40
upstream ENSMUSE00000647288 ChrY:732053..732259 CAGTGATGACGTGCCTGTAGA ChrY:732111..732131 59.91 52.38
upstream ENSMUSE00000647286 ChrY:730412..730548 GGGTCATCCCTGCATTAAAA ChrY:730462..730481 59.76 45
upstream ENSMUSE00000647284 ChrY:727718..727851 TCCCCGTGTATTTTATCGTCA ChrY:727816..727836 60.19 42.86
upstream ENSMUSE00000626480 ChrY:721713..721800 No primer for this exon
upstream ENSMUSE00000626479 ChrY:720635..720977 GGATGGTCAACTCTGGCTCT ChrY:720946..720965 59.26 55
upstream ENSMUSE00000626478 ChrY:719759..719854 GGTCCCAAATTGCAAGCTAA ChrY:719763..719782 60.07 45
upstream ENSMUSE00000626477 ChrY:717627..717841 TCTTGCTTTGATCGCTTGAA ChrY:717795..717814 59.69 40
upstream ENSMUSE00000626476 ChrY:704471..704711 ACGCTGCATTCTCAATCGTA ChrY:704581..704600 59.45 45
upstream ENSMUSE00000626475 ChrY:703499..703651 CTGATTCGTCAGCTGGACCT ChrY:703571..703590 60.41 55
upstream ENSMUSE00000626474 ChrY:701104..701224 GCATGTTGACTGTGCCAACT ChrY:701147..701166 59.76 50
upstream ENSMUSE00000568545 ChrY:693177..693307 GGTTCTTCTGCCTCCCAAGT ChrY:693193..693212 60.63 55
upstream ENSMUSE00000568544 ChrY:692582..692860 CCTTGTTAATGCCTGCTGGT ChrY:692831..692850 60.13 50
upstream ENSMUSE00000568543 ChrY:688593..688718 GGTGCTACAAAATGCCCTTC ChrY:688670..688689 59.57 50
upstream ENSMUSE00000568541 ChrY:688305..688430 GCAGCAGGATGTGGATCATT ChrY:688354..688373 61.05 50
upstream ENSMUSE00000568540 ChrY:686969..687138 AAGCCCTGGAAGTGATGACA ChrY:687067..687086 60.66 50
upstream ENSMUSE00000568538 ChrY:678215..678323 TGTTGCATGGGACATAGACC ChrY:678255..678274 59.37 50
upstream ENSMUSE00000568537 ChrY:677864..678010 TGCAGCTAACGAGAAGGGTA ChrY:677989..678008 58.67 50
upstream ENSMUSE00000568536 ChrY:676435..676581 AGGCCATCTGGGAGTAACAA ChrY:676512..676531 59.55 50
upstream ENSMUSE00000568534 ChrY:672707..672929 TCCTGCATCCAAAGCTTACC ChrY:672887..672906 60.21 50
upstream ENSMUSE00000568533 ChrY:670057..670277 TGTGGGACTGAAAAATGCTG ChrY:670194..670213 59.69 45
upstream ENSMUSE00000568530 ChrY:668764..668954 No primer for this exon
upstream ENSMUSE00000568528 ChrY:661302..661475 AATCTCCGTGAGCAACATGA ChrY:661437..661456 59.24 45
upstream ENSMUSE00000568526 ChrY:655500..655641 No primer for this exon
upstream ENSMUSE00000568523 ChrY:652906..653653 TGCAATTCCTGCATAACCAA ChrY:652985..653004 60.07 40
upstream ENSMUSE00000568521 ChrY:652368..652491 No primer for this exon
upstream ENSMUSE00000568518 ChrY:651006..651243 TCTGGAATGTCCAAGTGCAG ChrY:651122..651141 59.83 50
upstream ENSMUSE00000568516 ChrY:650171..650300 CATGGGCGACATTTACAACA ChrY:650206..650225 60.38 45
upstream ENSMUSE00000568513 ChrY:646953..647138 TGTCTTTGGATGAAGGACCA ChrY:647062..647081 59.06 45

*** Putative Vector Insertion (Chr Y: 646952 - 650301) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000568510 ChrY:644294..644514 TGAATTGGCATTATCGGTTG ChrY:644429..644448 59.38 40
downstream ENSMUSE00000568509 ChrY:644123..644211 CTTGCCAGGAGTCCTCAAAC ChrY:644108..644127 59.84 55
downstream ENSMUSE00000568507 ChrY:641056..641212 CTGCAAGATCTGGTAGGCAAC ChrY:641034..641054 59.89 52.38
downstream ENSMUSE00000568505 ChrY:640729..640941 CATTCCATAGCCCAAGTCCA ChrY:640876..640895 60.85 50
downstream ENSMUSE00000568504 ChrY:639816..639911 ATGTTCATCGAGGGCATCTT ChrY:639857..639876 59.51 45
downstream ENSMUSE00000568502 ChrY:635404..635540 CTGAAAACGGCTGTTCAGGT ChrY:635491..635510 60.29 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AATAATCGCCTTGCAGCACA ChrY:647232..647252 61.69 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GTCTACATTCGTGACTGGGAAA ChrY:647237..647259 59.1 45.46 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000069044