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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag

Basic information

species Oryza sativa
transcript LOC_Os02g50320.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G832989_T01 (Zea mays), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag
 ||||| || ||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||||  |||| || |  |      ||||  |  ||  |||| || ||| ||  |  |  || | |     ||| |    ||| | | || | | |  | || || ||||  ||
TGCAAATAGGGTTGCTGTTGTGGTCGCAAACGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTTAAACAGTGGCTGGAAGAGCGAAGGTTCCTGCAGgtag-gatgctaaagct------gtttcatatagggcatccacagttatcagtagagtgtaaaat---gcatta---gttctaatgttgtcg-acaaaaactgcttctgtag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatcta-cggttg--tccatg----caaagtcacacttcacat-catatattcaatttttatggcatgacaaatgtttcttcag--------------------------------
|||||||||||| |||||||| ||||||||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||| ||  | ||  |||||||||   |  | | |||   | ||    || |     || ||  |||||  | | ||    | | | | |  ||  | |  || | |||  || |  |    |  || || |  ||||                                  
AGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATAAAGTGATGCCTGTCAAACAGTGGCTTGAAGAACGTCGATTCTTGCAGgtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatact-tctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttat--ggcatgacaaatgtttcttcag-------------------
|||||||||||| ||||| || ||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||| ||  | ||  |||||||  | || || |    |   ||||  |||      |  |      || |  ||  |||     |  |  | || |  |||   |||   |     | |       ||| || |                    
AGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACAAAGTGATGCCTGTGAAACAATGGCTTGAAGAACGACGATTCTTGCAGgtggatatcatttctgattcctttggatttaatcttttgtgcctttttttttataaaaaaaagtatatatcttcttgcatttggtttcccttcaatacggtttccatttttttaccaaactacacttttattag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatcta-cggttgtccatgcaaagtca--cacttcacat-catatattcaatttttatggca---tgacaaatgtttcttcag--------------------------------
|||||||||||| |||||||| ||||||||||| ||||||||||| ||||| ||||| |||||||||||||| ||||||||||| ||| | ||  |||||||||   |  | |  ||   | ||    || |     || ||  |||||    |   || ||    |||     | | ||||||   ||||||| | |   |  |  || |  ||||                                  
AGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATAAAGTGATGCCTGTCAAACAATGGCTTGAAGAACGCCGATTCTTGCAGgtaatatttttttgttttactctgccaattcatctgaatttagtggttgagtttttgaattccattactctttctgcttatatttcttttttatagtaatttcccgcatctggcttcgctttccacttattattaaattgaattcttatag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgc-aaagt-cacacttcacatcatata--ttcaatttttatggcatgacaaatgtttcttcag------------------
|||||||||||| ||||| || ||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||| ||  | ||| ||||||| || ||    || ||||| ||    |||| |  | | ||   || ||   |   |||||  | |  |  |  ||| |   |||   ||  |||   |    | | | | || |                   
AGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACAAAGTGATGCCTGTGAAACAATGGCTTGAAGAACGACGATTTTTGCAGgtgaatat----tatttctgatt--cctttggatttaaactttcgtggttttttttaaagtatatatcttcctgcatttggcttccccttcaatgtggttttcattttgtttttaccaaactacactcttatag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 5'ss of exon 8
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagat-gatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaat-------ttttatggcatgacaaatgtttcttcag------
 |||| ||| |||||   |||||| ||||||||||||||||||| ||  || ||||| |||||||| || || ||||| ||||| || || ||||||||||| |   | |||||  |  | || |  || ||   ||    |   |||||  || || | |||||     |||  ||  || | |       || | |  |        ||||||||         
TGCAAGCAGGGTTGCAACTGTAGTGGCAAATGAGTGGAAAGATGGTAGCGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGATTTCTGCAGgttacttttgatattttatttttgggcttctgttact-gcttcgagttgtg-attcatattcacaggaaccattgtaacttgagtaagtgcattctttaaccattttcctgtttctttttggacag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 5'ss of exon 7
---------------------------------------------AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaa-gatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaa--atgtttcttcag
                                              |||||||||||||||  ||| || || || || ||||||||| ||||||||||||| |||||||| |  |||||||||||||| || || ||| ||||||| |  | ||||| |    | ||  | |||  ||  ||   | | | |    ||    | ||| | |||||      ||    ||  |  || ||  ||    ||||||   |||
AGAGAGGAAAATCCTTGAACGGGAATTGGCCCGTGCGAAGGTAAATGCAAACAGAGTTGCTACTGTTGTAGCTAACGAATGGAAAGATTCTAATGACAAAgtgatgcctgtaaggcagtggcttgaagaacgtagatttttgcaggtcattgctgataca----tattaatattt--aaattctcttgctgcttcaaattgtgattcata-ttcacggagattaacttatactattgccaccaccgttatgtttggacag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag
|||||||||||||||    || ||||||||||| |||||||||| |||||| ||||| |||||||| || || |||||||||||  | |||||||| |||||  |  |   |||    ||    ||||   ||  |  |  |     |    |   |||| |||     ||    |  ||  ||| | |     | ||   | ||  | |||
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttg-atatgattgccc-ttttcctaaatttgtggaatccagattctttgaagtgacaaag-gcacacaaccttacattctcactctttaactc-tcttcttgcag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G14840.1 (Arabidopsis thaliana), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaa-gatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaa--atgtttcttcag
 |||||||||||||||  ||| || || || || ||||||||| ||||||||||||| |||||||| |  |||||||||||||| || || ||| ||||||| |  | ||||| |    | ||  | |||  ||  ||   | | | |    ||    | ||| | |||||      ||    ||  |  || ||  ||    ||||||   |||
TGCAAACAGAGTTGCTACTGTTGTAGCTAACGAATGGAAAGATTCTAATGACAAAGTGATGCCTGTAAGGCAGTGGCTTGAAGAACGTAGATTTTTGCAGgtcattgctgataca----tattaatattt--aaattctcttgctgcttcaaattgtgattcata-ttcacggagattaacttatactattgccaccaccgttatgtttggacag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagat-gatata------cttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag
|||||||||||||||   ||| || ||||||||||||||||||| |||||| ||||| |||||||| || || ||||| ||||| || |||||||| |||||  |  | |||||       | |||  | | || ||    | ||   |   ||  |  ||   |    |  | || ||| || ||||    ||  ||  ||    ||  ||| | |||
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaa--attatttgcagtgagcaaggcccatccatatc-tacattctcacttcttg--atcctcaacttttttgcag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgtttt----ttgaagct--catctacggttgtccatgcaaag-tcac-acttcacatcatatattcaatttttatggcatgacaaatgtttcttcag-------------
 |||||||| || || || || || |||||||| |||||||||||||||||||| || ||||| || ||||| ||||| || || ||  | ||  |||| ||||| |   |  | ||||  ||||||      |  ||||   || ||| |||     | |   | |||  |||     |    | |  | |||  |  |  ||  || |||| |   |              
TGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACAAGGTGATGCCCGTAAAACAATGGCTAGAGGAACGGCGATTCTTGCAAgtaaatactctgaagttcttattgtttcaaaacttgagctattatttactgtttctttttctttgatcatgactgtgtttggcttttgtagtttccacagtttg-taattgttaccaaaacctcttgttacag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S31_77V6.1 (Physcomitrella patens), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgca--aagtcacacttcacatcatatattcaatttttatggca-------tgacaaatgtttcttcag------
||| ||||||||||| ||||| ||||||||||||||||| ||||| |||||||| || ||||||||||| |||||||| || ||| | |||||| |||||||     |||| |     | | |   |  ||||  | ||| |   |     | |||  ||   |||  |    |  | | |||  || | || |         |||  | |||   | |        
AGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACAAGGTTATGCCTGTCAAGCAGTGGCTCGATGAGAGGAGGTTTATGCAGgttcgtttgattttgcagtctgtacctcctgaatgttatcgattatgaggtaagcagtaaaatacaactttttttcttttttcttttctgattgtgagttttctgatcattgtcgttacgattacag

upper sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ18059 (Selaginella moellendorffii), 5'ss of exon 7
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag
|||||||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |||||||||||| | || ||  |||||||      | ||   || ||| ||  | | |    || || |   | | ||   | ||||     | |   |||                                      
AGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACAAGGTCATGCCCGTGAAACAATGGCTTGAAGAGAGGAGATTCATGCAGgtgcgtgcg-tacg-ttgtgtgtgcgtgt-gtgtttcttccat--tcggcctaactaagtgcgtgtccttgtcag-------------------------------------

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|58660861|gb|CK049541.1|CK049541
EST:     ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTGTGTGCAG                         GGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
genomic: ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatga ... gtttcttcagGGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
EST: gi|58661349|gb|CK050029.1|CK050029
EST:     ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAG                         GGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
genomic: ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatga ... gtttcttcagGGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
EST: gi|58681726|gb|CK070413.1|CK070413
EST:     ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAG                         GGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
genomic: ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatga ... gtttcttcagGGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
EST: gi|86495989|gb|CI138622.1|CI138622
EST:     ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAG                         GGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT
genomic: ACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatga ... gtttcttcagGGTGAGATGCAGCAACTTCGTGATAAACTTGCTATTGCAGAACGAACAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG