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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatcccctcgatctgcatccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta...

Basic information

species Oryza sativa
transcript LOC_Os09g38790.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcc--cccccccccccactttcctccccatcccc---tcgatctgcatccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta
||||||||||||||||||||||||| ||||||||||||||||||||||||   ||||||||||| ||||||||||||||||||||||||||||| |||||||  |  |  || |||| ||| || |||| | | |||||   |||||||||  | |  || |||  |     | |||| |    |  ||||   |          
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct-----

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA05G34280.1 (Glycine max), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatcccctcgatctgcatccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta------
| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||   |||     ||| |  ||| ||||  ||   || |   |      ||||   | |  ||       ||    ||   |   | ||  | |    |      
AAGCCAAGCACTTCAAGTGCCATGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTTCACAAGGAATCCGTCACTAAgtataaccctatttccctc--ttttctccttattatcttgggttag----ggttttctgctttacattttgttttatcattaatcatattaaacgaaaaaaaaagt

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA08G05390.2 (Glycine max), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatccc---ctcgatctgcatccggttcaatcccgtagcccgg---attcggccagcta---gatttttggatggcgta-------------------------------------------------------------------------
| ||||||||||| |||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||   |||     ||| |  ||| ||||  ||       | ||  |   |    | || |   ||   |  |   ||  ||  |   |   || | ||| |     |                                                                          
AAGCCAAGCACTTTAAGTGCCATGTCTGCCACAAGAAGCTCTCTACCGCTGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAATCCGTCACCAAgtataaccctatttccctc--ttttctccttatttagggtttgagttttctgttttacatttttgttttcttgttaatagggttaatcatcggaatattgaaatatatggaatgcaagggttaatcatccacgtccttttcacaacaaattgttgagattttccctttttattctttctcag

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatcccctcgatctg--catccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta-
|||||||||||||||||||||| |||||| ||||||||||||||||||||   |||||||||||||||||||||||||||||||||||| ||||| |||||||| |   | |  | |||| ||   ||    ||       |||   |||||  | |  | |   |||    |||  |   |     ||| |  ||  |    
AGGCCAAGCACTTCAAGTGCCATGTCTGCAACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGACCGTCTCCAAgtacttttgctcttctcccatttctttcgttttcattctactctattcatcctttccttttcttcagc---aattttggaggaattctttatcaatccctagc

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatcccctcgatctgcatccggttcaatcccgtagc--ccggattcggccagctagatttttggatggcgta--
|||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||||| |||||||||||||||||||||||| ||| ||||  ||||||||     | | |   ||  | | || || |     |  || || || | | |   ||  ||       |   | ||       | |||| ||     ||   
AGGCCAAGCACTTCAAATGCCATGTCTGTCACAAGAAGCTCTCCACCGCCGGTGGCATGGTCATCCACGTCCTCCAGGTCCACAAAGAGACCGTTTCCAAgtac----tctctcaaacctttcttcttcctaaattatacatatgtataccgcttgttcttgtgatggttgaccttggaatttgtggttttcggggattgtgag

upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ16991 (Selaginella moellendorffii), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatcccctcgatctgcatccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta
|||||||||| ||||| ||||| ||||| ||||||||||||||||| ||||| || ||||   |||| ||  | |||||||||||||||||| |||||||||| |     | ||  | |  |||| |     | | ||  || | | | || |||  | | |                                      
AGGCCAAGCATTTCAAATGCCATGTCTGTCACAAGAAGCTCTCCACTGCCGGAGGAATGGTTGTCCATGTTTTGCAGGTCCACAAGGAGTCCATCACCAAgtaaggatttctccttctc--tttcatat--gttctctaaattt-ctttcgcttctttgcag--------------------------------------

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|29655595|gb|CB651870.1|CB651870
EST:     CGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGTAGCTCCGTCACCAA                         GGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
genomic: CGGCATGGCCATCCACGTCCTCCAGGTCCACAAGG-AG-TCCGTCACCAAgtacgtcccc ... ttgaccacagGGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
EST: gi|29624560|gb|CB629571.1|CB629571
EST:     TGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAA                         GGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
genomic: TGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccc ... ttgaccacagGGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
EST: gi|29630516|gb|CB635525.1|CB635525
EST:     GGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAA                         GGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
genomic: GGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccc ... ttgaccacagGGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
EST: gi|58664656|gb|CK053342.1|CK053342
EST:     GGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAA                         GGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG
genomic: GGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccc ... ttgaccacagGGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcccccccccccccactttcctccccatcccctcgatctgcatccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG