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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATGTGTTGTTGGGGTTGCACGCACCCCTATGGGTGGTTTCCTAGGTGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccagtatcttctcatatgctgtatgtgtaattgttcttttaacccaaatataactaacatcatcagtgtggtgatcag

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 3
ATGTATGTGTTGTTGGGGTTGCACGCACCCCTATGGGTGGTTTCCTAGGTGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgatacc-----agtatcttctcatatgctgt--atgtgtaattgttcttttaacccaaatataactaacatcatcagtgtggt--gatcag----
|||||||||||||||| ||||||||||||||| ||||||||||||| |||||| ||||||||||| | || || || |||||||| ||||||||||||||||| | |     | | | || |  |  |||    |  |    |   | ||| | ||| ||||  |  |    ||| ||  ||||  |  | |    
ATGTATGTGTTGTTGGCGTTGCACGCACCCCTTTGGGTGGTTTCCTTGGTGCCTTGTCTTCCTTGCCCGCAACAAAGCTTGGTTCTATAGCAATTGAAGgtgacatccaaataatctttttttctgagctacgaacattctgtatctgtttcacccccaataacagcactgacatgagcatggttggggccgttag

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 2
ATGTATGTGTTGTTGGGGTTGCACGCACCCCTATGGGTGGTTTCCTAGGTGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccagtatcttctc---------atatgctgtatgtgtaat---tgttcttttaacccaaatataactaacat---catcagtgtggtgatcag-
|||| ||||||||||||||||||||||||||||| ||  ||||||| |||||  ||||||||||| | || || |||||||| || ||||||||| |||||||   |   ||||||||         || ||   | ||  |||    | ||  |||  ||| ||||  ||| || |   |||   || | || |    
ATGTTTGTGTTGTTGGGGTTGCACGCACCCCTATTGGCAGTTTCCTTGGTGCATTGTCTTCCTTGCCTGCGACGAAACTTGGCTCTATAGCAATTCAAGgtgagctccaaatcttctctgcatttacatctgagctctgaataagctatatttgtttcgccccaatagcactgacgtggccatggatgggctgttacct

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 3
ATGTATGTGTTGTTGGGGTTGCACGCACCCCTATGGGTGGTTTCCTAGGTGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccagtatcttctcatatgctgtatgtgtaattgttcttttaacccaaatataactaacatc-atcagtgtggtgatcag
||||||||||||||||||||||||||||||| ||||| |||||||| |||||| ||||| ||||| | ||||| |||||||| || |||| |||| ||||||| | | | ||||||||      || || |  |   |  || | |||      ||  ||     |  | ||            
ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccgaatcttctc------tgcatttacatccgagctctgaacatggtcatggctgggggctgttag------------

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|58685561|gb|CK074248.1|CK074248
EST:     TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAG                         CTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
genomic: TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccag ... tggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
EST: gi|29640957|gb|CB645964.1|CB645964
EST:     TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAG                         CTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
genomic: TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccag ... tggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
EST: gi|88387760|gb|CI585463.1|CI585463
EST:     TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAG                         CTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
genomic: TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccag ... tggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
EST: gi|300215898|gb|HO088524.1|HO088524
EST:     TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAG                         CTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
genomic: TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccag ... tggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
EST: gi|88300828|gb|CI589820.1|CI589820
EST:     TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAG                         CTGCTCTGAAGAGGGCAAATGTTGATC-AGCCCTTGTGCAAGAGGTCTTCT
genomic: TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccag ... tggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
EST: gi|58683479|gb|CK072166.1|CK072166
EST:     TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAG                         CTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT
genomic: TGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccag ... tggtgatcagCTGCTCTGAAGAGGGCAAATGTTGATCCAGCCCTTGTGCAAGAGGTCTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTATGTGTTGTTGGGGTTGCACGCACCCCTATGGGTGGTTTCCTAGGTGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccagtatcttctcatatgctgtatgtgtaattgttcttttaacccaaatataactaacatcatcagtgtggtgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG