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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaaataatattttgaattgatatttagctttcttcttggtcccttgcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT

Basic information

species Oryza sativa
transcript LOC_Os02g07880.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
gtcagtaaataata-ttttgaattgatatttagcttt---cttcttggtcccttgcttttctttc---atatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
    || | ||||  |||| || || |||||  ||||    | || | |||||||||||  |||     |||  ||    ||| ||||||||||||| ||||||||||||||  |||| ||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||||   ||||||||||
----gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
gtcagtaaataatattttgaattgatatttagctttcttc--ttggtcccttgcttttctttcat--atgctttcactttcat-cttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
|| ||||| || | |||     || |||||| |||| |||  | |  |||||||||  ||||  |   | |  |    || || ||| ||||||| || |||||||||||  |||| ||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||||   |||||||| |
gttagtaatta-tttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G17110.1 (Glycine max), 3'ss of exon 8
gtcagtaaataatattttgaattgatatttagctttcttcttggtcccttgcttttctttcatatgctttcact--ttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
||||||  |  |   | |   |   | || |  |    |  | | |   |   |  ||  ||  |   |    |  |   | || ||||| | ||||||||||||||| | ||||||||  | ||| ||||||||||||||||||||||||||||||||||||| |  ||||||   ||| |||| |
gtcagtgcaccaatctgt---tctcttttaaattgcaatgataggcatctatctcactcgcagctaactcatttggtgtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGATAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCATTCAGAGCTCGGGATATTACAT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
gtcagtaaataatattttgaattgatatttagctttctt--cttggtccctt--gcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
         | | |||||||||||  ||  || | | ||   ||      ||  || ||    | ||  ||||    | ||   || ||||||| ||||||||||| ||  | ||||||||| | || |||||||| ||||||||  |||||||||| ||||  || || || |||   |||||||| |
--------gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaattagcttatg-tctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G29670.1 (Glycine max), 3'ss of exon 8
gtcagtaaataatattttgaattgatatttagctttcttcttggtcccttgcttttctttcatatgctttcactttcatct--tcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
||||||  |  |   | |   |   | || |  |    |  | | |  ||   | |||  ||  |   |    ||   | |  | ||||| | ||||||||||||||| | |||||||| || ||| |||||||||||||||||||||||||||||||||| || |  ||||||   ||| |||| |
gtcagtccaccaatctgt---tctcttttaaattgcaatgataggcatttatctatctcacagctaactcgttttgtgtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGGTAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGATCATTCAGAGCTCGGGATATTACTT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G06790.4 (Glycine max), 3'ss of exon 7
gtcagtaaataatattttgaattgatatttagctttcttcttggtccctt---gcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
         | | | ||||||||   ||  || | | || ||      ||   || |||   | ||  |||||   | ||   || ||||||| ||||||||||| ||  | || |||||| | || |||||||||||||||||  |||||||||| || |  || || || |||   |||||||| |
--------gtgagaatttgaattctaatacagttcttttgttaacatttttcagcctttagctaattagcttttg-tctctgatttagATGGTTGATCCTGGTGGCATTGCAAACTGGTCACTAACTCATGTTGATTGGTCTGAGAGAAAATGGCACCCTAAATCATACAGGGCTCAGGATGTTACTT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G25870.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcagtaaataatattttgaattgatatttagctttcttcttggtcccttgcttttctttcatatgctttcact---ttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
|| |||  ||  | ||   |    || |||  |  |||| |  | | |||| |  |      | |   ||       |     |||||||| | |||||    || ||||| ||||||||||||||   |||||||||||||||| |||  |||||||||| | | ||  |||  |  ||  || | |
gtgagtctatt-tcttcacaccccatcttttacaatcttttaagcctcttgatgctgaaaagtgtttatttgtcggctcttctttcagATGATTGATCCCATGGGGATCTCAAATTGGTCAGTGACGTTTGTTGATTGGTCTGAACGAAGGTGGCATCCAAAGACATACGGAGGAAACGAGATTTCAT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtaaataat---attttgaattgatatttagctttc---ttcttggtcccttgcttttctttcatatgctttcactttcat-----cttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
|| || |   | |   ||| | ||  || |   |   ||    || || || | ||  || ||  | |||| |||    | | ||        |||||| | ||||||  ||| ||  |||| ||| | |||||| ||||||||||||||||  |||| |||||||||||    || |   ||   ||| | ||  
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtaaataatattttgaattgatattt----agctttcttcttggtcccttgcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
|| || | || |||       |   | |||    |||||||    || | | |||    |   | | ||  ||   | || |     ||||| | |||||||| |||||||| || |||||||| ||| ||||||||||||||||  | | ||||||||||| | | ||||||||    |||||  |  
gtgaggagattataacaactttctctcttttaaaagctttcactgtgattc-ttgtcccttaatgaaatctttgttccttaa-----agATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 3'ss of exon 8
gtcagtaaataatattttgaattg------------------atatttagctttcttcttggtcccttgcttttctttcatatgctttcactttcatc---ttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
||||| | || | | |||| | |                    | || | |  || | ||  | |||||  ||||   ||| |  |  ||||         |||||||| | ||||||  ||||||  | || ||||| ||||||||||| |||||||| |||||||| ||||||||||   | || || | |   || || |  |
gtcagcacattaaactttgtactctttttcccataaaaccttgtgttaaaccctcctattatttccttg--tttccaacatttcttcccactgctgctgctttcagATGATCGATCCTACTGGAATTGCAAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTT

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 3'ss of exon 8
gtcag---taaataatattt-tgaattgatatt-tagctttcttcttggtcccttgcttttctttc--------atatgctt-tcactttcatct-tcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
|| ||   || |||  |||| |   ||| |||| || ||||   ||  |  |    ||  || |||        ||||| || |  | |  || | ||||||  | ||||| ||||| ||  | || |||||||| ||||||||||| |||||||||| ||| ||||||||||  || || || |||   |||||||  |
gtgagatatatataccatttgttccttggtattatatcttttggctctgctctagtctcatcattcccaactgaatatggttctttcatctatttgtcagATAATTGATCCAGGTGGCATTGCAAACTGGTCAGTTACACATGTTGACTGGTCTGAAGCAAAGTGGCATCCAAAATCATACAGGGCTCAGGATGTTAATT

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|29662011|gb|CB658286.1|CB658286
EST:     AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGG
genomic: AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgtcagtaaat ... tcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGG
EST: gi|427667|gb|D23801.1|D23801
EST:     AGGGACGCAACTGTATTGNTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGNCACATGTTGATTGG
genomic: AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgtcagtaaat ... tcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGG
EST: gi|29663728|gb|CB660003.1|CB660003
EST:     AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTAGAT-CTCGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTG
genomic: AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgtcagtaaat ... tcatcttcagATGGTAGATCCT-GGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTG
EST: gi|86492716|gb|CI135349.1|CI135349
EST:     AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGG
genomic: AGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgtcagtaaat ... tcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttcttcttggtcccttgcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
                                    ctttcactttcatctt  CT-rich tract
                      ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaaataatattttgaattgatatttagctttcttcttggtcccttgcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT