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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG

Basic information

species Oryza sativa
transcript LOC_Os02g56000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
gaagaatattgctttggtccagtgttggtctattttc--ttcctttattggtt--cttctgcttgctg---ctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
      | || ||    | | | |  |||| ||||||  |||  |||||| ||  ||| |  | | |     ||||   | |||||  ||| || |||||| | ||||||||||| |||||||| || ||||||||  | ||||| ||||||||||| ||||||||| |||| |||||||| ||||||||||||||||| || ||||
------ttttcctgaaatactgcga-ggtcaattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttct-gcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
         |  ||   |       |  |   |||  |   | ||||  | | ||| |  ||    | |||    || |       ||  | || || ||||||||||| || ||||| ||||| ||||| ||||| |||||||| || ||||| || || || || ||||| |||||||| ||||||||||| |||||||
-gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 5
--gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtc-tatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
        |||| |  | |  || |  |    |||||  ||   ||   |  |||  ||  ||    | |||  ||| | || |    ||| | || || ||||||||||| || ||||| ||||| ||||| |||||||||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| |||||||
gtttcctctatttcacttgcacactactaccttatttgtttgtattcacg--tctcttgactgggtttggat-tataatgatctaacctgcaattttgtacagATGTTCATAGGAGATGGAGCAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgc-tgctagatacatatt-----aatgtctatgcgaatt---ggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
 |  ||| ||  ||  |   |   ||    | |  | ||  || ||         ||  ||  ||     ||  ||||     | | | | | |  |||   | |  | || | | | |||  |   ||||| |||||||| |||||||||||||| ||||| ||||| || || ||||| || ||||| ||||||||||| ||     
-atcaatctt-tttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTA--GCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
--gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatg-tctatgc-gaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
    | | ||||| | |   |  | ||| |  | ||| | | | |   |   |  |      ||   | || |   |  |||  ||||  | ||| |  | |||||||| || || || || ||||| |||||||  |||||||||||||| ||||| ||||| || || ||||| || ||||| ||||||||||| |||||||
atctatactattgttcta--cttgcgttaga-tgtttgcatacatgtctatgtgctgcatcagcatttgga-atggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattg-gtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
   | ||      | |    |  ||      |||||  || | |    ||  |  |  |||   | | |   | | |||  | | |  || ||  ||  ||||||||||||| ||||| ||||| |||||||||||||| || | ||||||||| ||||||||||| || || || || || ||||| ||||||||||| |
---gtatgaaaactagagtaaacgt-aactgattttgatcttgttcctgtgatattttttga-accaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------------------------------------gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattg-gtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
                                                                                  | || |||    || ||  |      |  |||   |      |    |  |  | |||| |  ||   ||||  | |  |  || | | ||   | ||||||||||| || || || |||||||||||||||||||||||||| ||||| || |||||| | || ||||| || || || |||||||| || || ||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaata-attacatgtgacgagctataatgatacttgattgtaatgacatgatgacat--atccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
-----gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
           |      | |      |||| || |  | | | | ||  ||| |   |    ||     || ||  |    ||   || || ||||   | ||||||||||| || ||||| || || |||||||||||||||||||||||||| || |||||||| || |||||||||||||| ||||||||||| || || |
aattctctagttgccatgtagcaattatgttagtgtgatgtgtgcattctttgatctattcttttat---taaatgtaaccaaacaact-tg-gaatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttctt-ctgcttgctgctagatacatattaat-gtctatgcgaattg-gtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
        || |  | ||  |   |  | || |         || ||  |  || |   ||     ||     | ||||||  |||    | | ||  ||||||||||||| || ||||||||||| ||||| || ||||| || ||||||||||| ||||||||||| || |||||||| |||||||||||||| || ||||
---attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
                                      | || | | ||  ||  |  |  |||   | | | ||          |  |  | |   |||||||||||||| ||||| |||||||| ||  | |||||||||||||| ||||| |||||  | |||||||||||||| || |||||| | ||||| ||||
-------------------------------------gttctgtgtaggaactctt--tacctgtcgggttcttaaactcaagcttctggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttct-tctgcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
                                      | || | | ||  || | | | ||  |     |  |  | ||  |   ||    | | | |||||||||||||| ||||| |||||||| ||  | |||||||||||||| ||||| |||||  | |||||||||||||| || |||||| | ||||| ||||
-------------------------------------gttctgtgtaggaactctttacctgtcgggttgttaaactcaagcttcttgt---tcgttgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

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|3759941|gb|C97199.1|C97199
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29660288|gb|CB656563.1|CB656563
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGGTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29682547|gb|CB678822.1|CB678822
EST:     CCCAAACTAACGCCACATTTGTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29659489|gb|CB655764.1|CB655764
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29626138|gb|CB631149.1|CB631149
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29661398|gb|CB657673.1|CB657673
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29659490|gb|CB655765.1|CB655765
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29615761|gb|CB620773.1|CB620773
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|11173135|gb|AU164630.1|AU164630
EST:     CATTTNTGAAACTTGCTGGTCCACAGCTTGTCCAA                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29615719|gb|CB620731.1|CB620731
EST:     CCCAAACTAACGCCACATTTTTGAAACTTGTTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGGGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29683382|gb|CB679657.1|CB679657
EST:     AGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: AGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29682519|gb|CB678794.1|CB678794
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29683381|gb|CB679656.1|CB679656
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29615715|gb|CB620727.1|CB620727
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29684874|gb|CB681149.1|CB681149
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
EST: gi|29615721|gb|CB620733.1|CB620733
EST:     CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAG                         ATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA
genomic: CCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgtagcttact ... attggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttcttctgcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG
                            tattaat  putative branch site (score: 2)
                    tagatacatattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA