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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA

Basic information

species Oryza sativa
transcript LOC_Os04g47240.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 4
gaagttgcatgatagcatctaggatttcattaat-gagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
||   | ||  | ||| | |   || |||||||| | |||||  ||| |  | |||  |||||      ||   | |   ||||| | ||||| ||   ||||||| ||||| ||||| ||||| ||||| ||||| ||||||||||| || ||||||||||||||||| ||||||||||||||||||| |||||||||||
gagagttcacaacagcttgtcacatatcattaatagggttatggatgcattattttc-atttttaggcatgaacttatacattatgtttgcccaaaattagGTTGAAGATAAACTTTACATATATTTGGAATATGTTTCTGGTGGATCCATACATAAACTTCTACAAGAATATGGACAGCTTGGTGAACCAGCAATACGCA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 6
gaagttgcatgatagcatctaggatttcattaatg-agttatttatgtaccacttttgattttct---tttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
   ||| | || | |  | |  |||  |||  | |  |  |||| |  ||    |||| |||| |   |  ||       ||| | | | |  ||   | |||||||||||| |||||||| |||||| | || ||||||||||| || || || ||||||||||| ||||| ||||| ||  ||||||||| ||  || || |
--tgtttc-tggtggtttatctgataacatagaagtgggaatttctcgacagtatttgtttttgtggttccttatagaggcttctgaatcgccccttga-acagGTTGATGACAAGCTTTACATATACCTTGAATATGTATCTGGAGGCTCCATACATAAACTTCTTCAAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
-----gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
     ||| ||  |  ||    |  |  | |  ||   | ||  |      |   ||||  |||| | ||   ||  ||   |   | ||| |      | |||||| ||||| || ||||||||||||||||||||||| |||||||| || ||| ||||  | || ||| ||||||| |||||| |||||   |  || || |
ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgattta--tggctctttataat---aaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 7
gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgcccca----atacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
    ||  |  |   |  | |     | |   |  |  |||||| |      | |||||  |     |||  || | | |||  | || |   |    | |||||| |||||||| ||||||||||||||||||||||| |||||||| || ||| ||||  | || ||| ||||||| |||||| |||||   |  || || |
----ttttagaaattcgacaatctactaaaatactaaatatttaagagaagatgttgatacttcagattgtttttagtgattcatggttctttataataaacagGTAGATGATAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
gaagttgcatgatagcatctaggatttcattaatg-agttatttatgtaccacttttgattttct---tttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
   ||| | || | |  | |  |||  |||  | |  |  |||| |  ||    |||| | || |   |  ||       ||| | | |    ||   | |||||| ||| | |||||||| |||||| | |||||||||||||| || || || ||||||||||| | ||| ||||| ||  ||||||||| ||  || || |
--tgtttc-tggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttccttatagaggcttctaaatcaccccttga-acagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
-gaagttgcatgatagcatctaggatttcattaatgagttat-ttatgtaccacttttgattttcttttt--------tggcttcacttattatttgtgcc--ccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
  |||||  |        ||| |||  |   |  |   | ||  |||  ||   ||  | |   |    |        || ||  | |  ||| ||   ||  ||||| ||||| ||||| ||||| ||||||||  |||||||||| || ||||| || ||| |||||||||| ||||||||||||||  |||||||  | || || || |
gtaagttttacagatatttcttggacatttctgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 4
---gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
   | | |    |   | ||| |   || | ||   | ||||     | |     || |  | || | |  ||   | || |   | || | ||   | |||||||| ||| || |||||||||||||||||||||||||||||||| || ||| |||||||||| ||||| ||||| || |||||||||| |||||| || |
tttgcaatattgttgcatcatgtgcaatattatgtttcagttggcacttt--tggttatcgtcttttgtactgatataacctcccaattattccatga-acagGTTGGTGACAAACTTTATATATACTTGGAGTATGTATCTGGTGGCTCCATCTATAAACTTCTTCAAGAATATGGCCAACTTGGTGAACTAGCAATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 3
------gaagttgcatgatagcatctaggatttcatta-atgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
      |||||| |||    ||||     |||  |||| || | |   |   |    | | || |  || | |      |||  |   ||| |    ||    |||||| ||||| || || || ||||| | ||| ||||||| |||||| || ||  |||||||||| ||||||||||| ||| ||||||||  ||| || |  |
tcctttgaagtttcat--ctgcatt--acattatattagatcactagatggcgattgattcttcagcttatgtgaaattttccttggctatat---tccttgaacagGTGGATGACAAACTCTACATATATTCGGAATATGTATATGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGTTTGGTGAAATAGCTATTCATA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 6
------gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
      |||| | |||    ||||     |||  ||||      ||  |    |    || |     |  | |     ||  |||    | | | ||   | |||||| ||||| || || || ||||| ||||| |||||||||||||| || ||  |||||||||| ||||||||||| ||||||||||||  ||| || || |
tcctttgaagcttcat--ctgcatt--acattatattagaacactagatggcgattgattcttcagcttatgtgaaattttccttggc-tatattccttga-acagGTGGATGACAAACTCTACATATATTTGGAATATGTATCTGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGCTTGGTGAAATAGCTATTCGTA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S44_113V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcact-tattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
                           ||  |  |  ||  | |||   |  |  | | |   |||||  |||  |  |   |      | |   |   | |||   |  || |   |      ||| | || |||| | | |||||||| ||||||||||| ||||| ||||| ||||||||||| || |||||||||||     |    || | ||   | ||||
gtgcgacgcaaaccttatgcaccttttaatatttaacatgacgtctgtcacatgttaactccattattcttgttgctttggggtcgacatgtcgggatctgactgcgtcgttgggatcttctggcagTTGGAAGATAGGTTGTATATATATTTGGAGTATGTTTCTGGAGGATCAATCCATAAACTGCTCCAAGAGTATGGCGCTTTCAAAGAGCCAGTGGTGCGCA

upper sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S8_299V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------gaagttgcatgatagcat--ctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
                    |   |||  | ||||  |  || |  |   |||     |    || ||   |  |    |||   |  |     ||     ||  |   ||      |  || | || || | | | |||||||| || |||| ||| || |||||||| ||||||||||| || |||||||||||     ||   ||||  |   ||||||
gtaccacgaaatctttgatagcttttgattcatagtgtgactggagtagtattgtgatgagtgttttgcggctgtggaaattgaatcgtccacatttgacgatgttgcttgggtttgtgtagTTGGAGGACAGGTTGTATATATATTTAGAGTTTGTCTCAGGTGGATCAATCCATAAACTACTCCAAGAGTATGGCGCTTTTAAAGAACCGGTTGTACGCA

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|58611652|gb|CK039364.1|CK039364
EST:     TGAGCCGCCTACAGCATCCAAATATCGTACAATACTATGGATCAGAAACG                         GTTGATGATAAGCTTTATATACTACTTGGAGTATGTATCTGGTGGATCTAT
genomic: TGAGCCGCCTACAGCATCCAAATATCGTACAATACTATGGATCAGAAACGgtataaatgc ... cccaatacagGTTGATGATAAGCTTTATATA-TACTTGGAGTATGTATCTGGTGGATCTAT
EST: gi|4715352|gb|AU056469.1|AU056469
EST:     TGAGCCGCCTACAGCATCCAAATATCGNACAATACTATGGGTCAGAAACG                         GTTGATGATAAGCTTTTATATATACTTGGGGTATGTATCTGGTGGNTCTAT
genomic: TGAGCCGCCTACAGCATCCAAATATCGTACAATACTATGGATCAGAAACGgtataaatgc ... cccaatacagGTTGATGATAAGCTTT-ATATATACTTGGAGTATGTATCTGGTGGATCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
       ttttgat  putative branch site (score: 4)
       ttttgattttcttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA