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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAACTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094712_T02 (Zea mays), 3'ss of exon 4
gtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgacca-attgtaacaaacagtaaaattatctcactaagataacttct--------tcagatcctttgctact---tttggcttattc---ttgtattaggtaattcacaaaactgattatactatttattggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAACTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA
  |  |||    | | |    | ||     |    |  |||     ||   |     | |      |||    ||| || || |  |     | |  |  | |          | || ||| | ||||||   | ||| ||||||   || |||||  | ||| |   | |||||| |  | || | | ||| || ||||| ||||| ||||||||||| ||||| || |||||| | || || |||||||||||||| || ||||||||||||||||||||||| ||||| || 
--gtattctctgtttgactggtttacccattttcctcatttgtgggtcaactgttcctaatggtgatgttgtcaactgtgaattcttagtgttgaagtttcattacataaaaataagttccctagctactggttctggtttattcaggttttattacttcatt-agggagctgattttttttttgaatcgaatagCCCTGCTATTCAGGAGAATAGGGTTGCTACCGTGCAGTGCCTATCGGGTACTGGTTCTTTAAGAGTCGGAGGTGAATTTCTTGCAAGGCACTATCACGAG

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G08670.2 (Glycine max), 3'ss of exon 4
gtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAACTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA
                                                                                       | | ||| | ||          |  |||  |  || |      || |  || |  |||  | |         || ||| |||| |||  | || ||||| |||||||| || |||||  | || ||||| |||||||| ||||||||||||||||| || || ||||||||| | || |  || |||||  ||
--------------------------------------------------------------------------------------gttaataatagaaacaaaatcagtggtttcttgtttgtaaagatttttcctaatcagtacctaattgtttatgttttac-attttttgtcatagCCCTGCTATTCAAGACAACAGGGTTACCACTGTTCAATGCTTGTCTGGAACTGGTTCTTTAAGAGTTGGGGGTGAATTTTTGGCTAAACACTATCACCAA

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G08560.1 (Glycine max), 3'ss of exon 4
gtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAACTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA
                                                              |||  ||| ||||| || || |   |   |        ||  | |     ||||||  |     | || | || | |        | |||        | |  | ||| |||  | || ||||| |||||||| || |||||  | || ||||| |||||||| ||||||||||| ||||| || || ||||||||| | || |  || |||||  ||
-----------------------------------------------------------gttaataataa-aaacaatataagtgctttcttg-------tttgtaaagatttttgctgatcagtacctaattttttgt------gcttaca--------tttttttttttttgttatagCCCTGCTATTCAAGACAACAGGGTTACCACTGTTCAATGCTTGTCTGGAACTGGTTCATTAAGAGTTGGGGGTGAATTTTTGGCTAAACACTATCACCAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32948428|gb|BP185000.1|BP185000
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33685641|gb|CF313880.1|CF313880
EST:     CTGGCCGATTTCAATAAGCTTAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|44667509|gb|CR280943.1|CR280943
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33678230|gb|CF306469.1|CF306469
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33794428|gb|CF323098.1|CF323098
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|58591056|gb|CF989364.1|CF989364
EST:     CTGGCCGATTTCACTAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGACTAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|27576897|gb|CA999591.1|CA999591
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|32948311|gb|BP184883.1|BP184883
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|218483959|gb|FG947666.1|FG947666
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33793733|gb|CF322749.1|CF322749
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33794958|gb|CF323359.1|CF323359
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|58656014|gb|CK044694.1|CK044694
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|29679665|gb|CB675940.1|CB675940
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|163926589|gb|EG713605.1|EG713605
EST:     TTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: TTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|2310086|gb|C26241.1|C26241
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|218478855|gb|FG949686.1|FG949686
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCA
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCA
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33678676|gb|CF306915.1|CF306915
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|10794714|gb|AU108680.1|AU108680
EST:     CTGGCCGATTTCAATAAGCTGAGTNCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
EST: gi|58669037|gb|CK057723.1|CK057723
EST:     CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAG                         TCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC
genomic: CTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcct ... attggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattcttgtattaggtaattcacaaaactgattatactatttattggaacagTCCTGCCATTCAAGAGAATAGGGTGGCTACAGTTCAGTGCTTGTCAGGAACTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA
                            aactgat  putative branch site (score: 3)
                          aaaactgattatacta  TA-rich tract