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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGATGGGATATAAGATGTTTGGTGAGTCCACTGAATCTCAGTTCACGCTGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaaaactctttcaaacatttcctttaattactatgctataaccatacaaatgggtcagaaacttatgtttgcttattacctgggataatcatg...

Basic information

species Oryza sativa
transcript LOC_Os02g01100.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01100.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G105192_T03 (Zea mays), 5'ss of exon 6
TGTGATGGGATATAAGATGTTTGGTGAGTCCACTGAATCTCAGTTCACGCTGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaaaactctttcaaacatttcctttaattactatgctataaccatacaaatgggtcagaaacttatgtttgcttattacctgggataatcatg------
 ||||||||||| || |||||||||||  ||||  | |||||||| || |||||||||||||||||||| |||||||||||| |||| || ||||||||||||||       || | | || |||||     |||| |  | ||| ||  |    ||  |  | |||  ||  ||||||||| | | ||| | ||| ||       
GGTGATGGGATACAAAATGTTTGGTGAAGCCACACAGTCTCAGTTTACACTGAACTTACCAGAGAATTTAGTGGTTTCAAAGATTGCAGTTTGGACCACGgtaattttcg--ctgtataaaccatttg---aaatttcatttcta-aaagaagttaagagacctgaacttttggtttgcttagtgcatggaacaatgatatcatgg

upper sequence: LOC_Os02g01100.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G134888_T01 (Zea mays), 5'ss of exon 7
TGTGATGGGATATAAGATGTTTGGTGAGTCCACTGAATCTCAGTTCACGCTGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaat-gcca------aaactctttcaaacatttcctttaattactatgctataaccatacaaatgggtcagaaacttatgtttgcttattacctgggataatcatg
 ||||||||||| || |||||||||||  |||| || || || ||||| || ||||||||||| ||||  ||  |||| ||| ||||||| ||||| |||||||| |         ||||  |||||||    || || |    ||  |    ||  ||  ||     |   ||| ||||  |   | |  | ||    |||     
AGTGATGGGATACAAAATGTTTGGTGAAGCCACAGAGTCCCAATTCACACTCAACTTACCAGATAATTCTGTCATTTCTAAGATTGCTGTTTGGACAACGgtaattgttgcttgataaaccttttcaaattcctctttcaccccctccgtctcaa--attaaatcaacttctaaagttatcctaagtca--aactattttaagt---
















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|29678444|gb|CB674719.1|CB674719
EST:     TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACG                         GTGGCAAATCCAATAACCAA
genomic: TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaa ... tttgttgcagGTGGCAAATCCAATAACCAA
EST: gi|27548100|gb|CA766182.2|CA766182
EST:     TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACG                         GTGGCAAATCCAATAACCAA
genomic: TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaa ... tttgttgcagGTGGCAAATCCAATAACCAA
EST: gi|87006659|gb|CI295042.1|CI295042
EST:     TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACG                         GTGGCAAATCCAATAACCAA
genomic: TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaa ... tttgttgcagGTGGCAAATCCAATAACCAA
EST: gi|86498766|gb|CI141399.1|CI141399
EST:     TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACG                         GTGGCAAATCCAATAACCAA
genomic: TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaa ... tttgttgcagGTGGCAAATCCAATAACCAA
EST: gi|29663318|gb|CB659593.1|CB659593
EST:     TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACG                         GTGGCAAATCCAATAACCAA
genomic: TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaa ... tttgttgcagGTGGCAAATCCAATAACCAA
EST: gi|29659581|gb|CB655856.1|CB655856
EST:     TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACG                         GTGGCAAATCCAATAACCAA
genomic: TGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaa ... tttgttgcagGTGGCAAATCCAATAACCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGATGGGATATAAGATGTTTGGTGAGTCCACTGAATCTCAGTTCACGCTGAACTTACCAGAGAATTTGGTGGTTTCAAAGGTTGCTGTCTGGACCACGgtaatgccaaaactctttcaaacatttcctttaattactatgctataaccatacaaatgggtcagaaacttatgtttgcttattacctgggataatcatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG