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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatgtgccagtgtgacatgcaattgtttgaattcagaatctctattttgtttttacatttttatgtgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGAGACATATATGACCAATATGGGGAGGATGCTCTTAAGGATGGAATGGGAG

Basic information

species Oryza sativa
transcript LOC_Os04g46390.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G14540.2 (Glycine max), 3'ss of exon 2
-------------------gtgaggatgtgccagtgtgacatgcaattgtttgaattcagaatctctattttgtttttacattttt-atgtgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGAGACATATATGACCAATATGGGGAGGATGCTCTTAAGGATGGAATGGGAG
                    |  |  ||    | ||  |  |    ||  |   | |     | ||| ||||  |  || || | | ||   | |  ||||| || || |||   ||||| ||||| ||| | | |||||||||||||| |||| | |||||||| ||||| || ||||| ||||| || |||||||| |
atgttcactcgctaactttttatgattgaaaaactgctaagttttcttactgctactgcatttttctgttttaatactaaatatctgattcatatatcagTTCAAGGAGTTAGGTCAAGCATATGAAGTTTTAAGTGATCCTGAGAAGAAAGACCTGTATGACCAGTATGGTGAAGATGCCCTTAAAGAAGGAATGGGGG

upper sequence: LOC_Os04g46390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S342_16V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------gtgaggatgtgccagtgtgacatgcaattg---tttgaattcagaatctctatttt----gtttttacatttttatgtgt-tttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGAGACATATATGACCAATATGGGGAGGATGCTCTTAAGGATGGAATGGGAG
             |  ||   |||  | ||||  |||  |  |    ||||| |  | || |   | |     |   | | |  ||||||| |  || |||||||| ||| |  | || || || || ||| | | ||||||||||||| | || |||||||| |||||||| || ||||| ||||| || |||||||| |
tgtagacatggctgcaagctcgtgt-actgtggtatgagagagggacttgaacttgggatttaattctctggagggctgagacgtttatgtatgcttgcagTTTAAGGAACTTGCTCAGGCTTACGAAGTTTTGAGTGATCCTGAGAAGCGTGATATATATGATCAATATGGTGAAGATGCACTTAAAGAAGGAATGGGTG
















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|29678521|gb|CB674796.1|CB674796
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|33694058|gb|CF322297.1|CF322297
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|218494200|gb|FG946885.1|FG946885
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29678572|gb|CB674847.1|CB674847
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|13807441|gb|AU181957.1|AU181957
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29637040|gb|CB642049.1|CB642049
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|14714017|gb|AU197958.1|AU197958
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|33657288|gb|CF279902.1|CF279902
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29663531|gb|CB659806.1|CB659806
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|33657059|gb|CF279673.1|CF279673
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|88352585|gb|CI624524.1|CI624524
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
EST: gi|33657234|gb|CF279848.1|CF279848
EST:     GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAG                         TTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA
genomic: GGAAGGCTGCCATAAAAAACCATCCTGACAAGGGAGGGGATCCAGAAAAGgtgaggatgt ... tgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtttgaattcagaatctctattttgtttttacatttttatgtgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGAGACATATATGACCAATATGGGGAGGATGCTCTTAAGGATGGAATGGGAG
                      tattttgtttttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggatgtgccagtgtgacatgcaattgtttgaattcagaatctctattttgtttttacatttttatgtgttttacagTTTAAAGAATTATCACAAGCGTATGAGGTTCTCACTGATCCTGAGAAGAGAGACATATATGACCAATATGGGGAGGATGCTCTTAAGGATGGAATGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA