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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacag

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G094712_T02 (Zea mays), 5'ss of exon 4
GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcctgctctcaagaatatatatggtcat-atggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttct--------tcagatcctttgctact---tttggcttattc---ttgtattaggtaattcacaaaactgattatactatttattggaacag
||||||||| ||||||||  | || ||||| || ||||| || |||||||||||||| ||||||||||| ||||| ||||||||||    ||    |  |  |  ||   ||  || | ||   |   ||| ||||| |   ||   |  |||    ||| || || |  |     | |  |  | |          | || ||| | ||||||   | ||| ||||||   || |||||  | ||| |   | |||||| |  | || | | ||| ||
GTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGgtattctctgtttgactggtttacccattttcctcatttgtgggtcaactgttcctaatggtga--tgttgtcaactgtgaattcttagtgttgaagtttcattacataaaaataagttccctagctactggttctggtttattcaggttttattacttcatt-agggagctgattttttttttgaatcgaatag

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G08560.1 (Glycine max), 5'ss of exon 4
GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacag
||||||    ||||| ||| | |||||   ||| || || ||||| |||||  ||||||||||||| |||||||| ||||||||||              || |||| | |   |   |  | || ||  | ||| |     ||    |  | |  |  |   || || |    || | ||   || ||       |||| ||                                                             
GTCACGCAACAAGGAATATATTCCGATTGTTGGGCTAGCTGATTTTAATAAATTGAGTGCTAAGCTCATTTTTGGGGCTGACAGgt-------------taataataaaaacaatataagtgctttcttgtttgtaaa----gatttttgctgatcagtacctaattttttgtgcttacatttttttttt------tttgttatag----------------------------------------------------------

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA06G08670.2 (Glycine max), 5'ss of exon 4
GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacag
||||||    ||||| ||| | ||||||  ||| || || ||||| |||||  |||||||||||||||||||||| ||||||||||       |  |   |  || | |    ||  | |  | |    |    ||     | | ||   ||| | ||  ||  |  | |  || |        ||  ||| |                                                                       
GTCACGCAACAAGGAATATATTCCGATCGTTGGGCTTGCTGATTTTAATAAATTGAGTGCTAAGCTTATTTTTGGGGCTGACAGgt-------taataatagaaacaaaatcagtggtttcttgtttgtaaagatttttcctaatca---gtacctaattgtttatgttttacatt-------ttttgtcatag----------------------------------------------------------------------

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv11s0016g03720.t01 (Vitis vinifera), 5'ss of exon 4
GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcg----ttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacag
||| || || || |||||  | || ||   ||||||||| || ||||||||  |||| ||||| || |||||||||||||||||||  |    || ||  ||| | ||| ||| | || | |   | ||  |  || ||  | |   |   ||  ||   |    |    ||   |    | | |||    ||    |  | | ||    ||  | |  | |  |  |  | | || |  ||| | ||| | || | | | | |||||
GTCCCGGGTCAAAGAGTACCTTCCCATTGTTGGACTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaactttctaatctgaggaa-ata-agggacttggtgctttgtattcagtagcataaaaaatatgctatatagattttgtgttgaattgtaaggttaaagcgttgcattattcttctggactt--cctgatatgattgtttggagtttattaaagt-attgtgctttatctggcaacag

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACGTGTTAAGGAGTATTTGCCGATCACTGGACTGGCCGATTTCAATAAGCTGAGTGCTAAGCTTATTTTTGGTGCTGACAGgtgcgttcctgctctcaagaatatatatggtcatatggtttcctcatctgttacctttgaccaattgtaacaaacagtaaaattatctcactaagataacttcttcagatcctttgctacttttggcttattcttgtattaggtaattcacaaaactgattatactatttattggaacag

- - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA