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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattatccagcactatgcttttctgtggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG

Basic information

species Oryza sativa
transcript LOC_Os12g06810.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G167999_T01 (Zea mays), 3'ss of exon 5
gta-tattatccagcactatgcttttctgtggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
||| |||||||||    | ||||||||||||| | |      |||| || |||  ||||  |   |||||||    || || | |||||||||||||||| ||||||||||| ||||| |||||||| || || |||||||||||| || ||||||||||||| ||||||||||| |||||||||||||
gtaatattatccacacttgtgcttttctgtggtatt------tttagccttttcattttttacagttttttt--gcctttgaattgtagAGCAATATTGTAGCCTCTGGTGGTCTTGGTGGTGAGGTTTTCATTTGGGACCTTGATGCTGCTCTTGCTCCTGTAGCCAAATCTGTGGATGCAAAAGAGG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------gtatattatccagc--actatgcttttctgtggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
                                                                         ||     ||  ||     ||     ||  || ||| ||    | |  ||   |   || |       |||  |  |    |||| | ||||||||||||||||||||||||||||||||||| ||||| |||||||||||  | ||  || |  |  |||| ||  | || |     ||||| | |   |
gtaatgtacttcaaacatcttatgcttcttattaagtgtgtcaagaaaaaagttcattttattgtttttatacgttccacattgagtcagatagaaactttggttgaattatcagtatcgtcaaatccattatttgatcgtttaatagtgtcatgcattttagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGGGAGGTTTTTATATGGGATATCGAGGCTGCCATCACTCCGGTTTCTAAGTGCAATGATGCTACAATTG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G40440.4 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------gtatatt----atccagcactatgcttttctg-tggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
                                                                            |||  |    ||  | ||    |||  | || | ||| ||   || | |   |  || ||| |      |||  |  |    |||  | |||| ||||||||||||||||||||||||||| || ||||| |||||||||||  | ||  || | || ||||| ||  | || | |   ||||  | ||  |
gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgtttctatatgctccacattaaacagatagctactttggttgaattatcaatgtcaaatccattctttgat---cctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------gtatattatccagcactatgcttttctg-tggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG---
                                                                          |  |   |  | ||    |||  | || | ||| ||   |||| |   |  || ||| |      |||  |  |    |||  | |||| ||||| ||||||||||||||||||||| || ||||| |||||||||||  | ||  || | ||||||||     | || | |   ||||| |  |  |   
gtaatgtactccaaacatcttatgcttcttattaagtgtatcgagaaaaagttcattttattgtttctatatgctccacattgaaacagatagctactttggttgaattatcaatttcaaatccattctttgat---cctttaatagtgtcttgctttttagAACAATACTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTTGCTCCCT---CTAAGTGTAATGATGCTATGGTTGATG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------gtatattatccagcactatgcttttctgtggaact---actc---attttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
                                                                          ||| |  || |  |  |     ||   | ||| |   | |    || |||||   |   ||||     | |||     |    || | | ||||||||| | ||||||||||||||||||||||| ||| | |||||||||||  ||||  || | || ||| | |   | ||||     ||| |||  || |
gtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttttcttcttgtttttatgtgctcaaatatgacatagtttgattgaatttaaagtttgaatcttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGATCCAATGGATG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G40360.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------gtatattatccagc--actatgcttttctgtggaactactcattttatcccttttgtt--ttacatgttttttt--ttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
                                                                        ||     ||  ||     ||     ||  || ||| ||    | | | |  |    |   |||  || |  |||  |  |    |||| | ||||||||||||||||||||||||||||||||||| ||||| |||||||||||  | ||  || | ||  |||| ||  | || |     ||||| | ||  |
gtaatgtacttcaatcatcttatgcttcttattaagtgcatcaagaaaaagttcattttattgtttttatacgttccacattgagtcagatagatactttggttgaattatcagtatcaactgtcaaatccattatttgatcgtttaatagtgtcatgcattttagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCACTCCAGTCTCTAAGTGCAATGATGCTACAGTTG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------gtatattatccagcactatgctt----ttctgtggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
                                                | |||     | |   || |     || || |||  ||     ||  ||  | | |  ||     | | | || |||        | ||||  ||| ||||||| |||||||||||||| || ||||| |||||||||||  ||||  || || |  | || ||  ||||| ||   || || || || |
gtaatttctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgattggtatggtggtgcaagttttgaggatatatgtgcttc-tcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------gtatattatccagc---actatgcttttctgtgga-acta---ctcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
                                                                                || |  | | ||     |   ||| | | || ||  | |    |  ||||| ||  | |  ||||       |||| |  |    |||| | ||||||||| |||||||||||||||||||||| || ||||| ||| ||||||| || ||  || | ||  |||| ||  | || ||    |||||||  ||||
gtaatttctttgtcaaaattttcatggaattatttactgcatagatgaagggttcttgtcagtgtaatgctgttatttaagtttcatgttcaatttaatggtgcatatttgggggcattgtgtcatattttgtcgttatcattttctgatccttttatagtgtcatgcattttagAGCAATGTTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTGTATGGGATCTGGAAGCTGCACTAACTCCAGTCTCAAAGTCAAGTGATGCAATGGAGG

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|117217320|gb|CT852008.1|CT852008
EST:     TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGNNNNNNNT                         AGCAATATTGTTGCCTCTGGTGGCCTTGGTGGTGAGGTCTTTATATGGGAC
genomic: TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGAAAAAAATgtatattatc ... tgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC
EST: gi|87023589|gb|CI286340.1|CI286340
EST:     TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGNNNNNNNT                         AGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC
genomic: TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGAAAAAAATgtatattatc ... tgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC
EST: gi|29666968|gb|CB663243.1|CB663243
EST:     TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGNNNNNNNT                         AGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC
genomic: TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGAAAAAAATgtatattatc ... tgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC
EST: gi|29678629|gb|CB674904.1|CB674904
EST:     TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGNNNNNNNT                         AGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC
genomic: TCCGCCAGCATTCCGATTATGTGATTTGTCTTGCTGCATCTGAAAAAAATgtatattatc ... tgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
            tcccttttgttttaca  CT-rich tract
                ttttgttttacatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattatccagcactatgcttttctgtggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG