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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattactattcgaactccgttgctgttgtctgtacctctgttgcagaagataaatcaaatttatttttgccatccactag

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47225.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 15
TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattactattcgaactccgttgctgttgtct--gtacctctgttg------cagaagataaatcaaatttatttttgccatccactag
||||| ||||||||||| ||| ||||||||||||||||  ||||||| ||||||||||| ||||| ||||||| | || |  |   |||   ||  |  || |   || |   | |||      ||| |    ||| |  |||  | || ||      |||
TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCACAGAAGTCCTCCAGCATACCTTCTTCCAGgtaacagtattccttctactttatttttagtggcaaggttcagttattgtctcctcagcactgtaataagttttcctgttacccatatttag

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 14
TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattac--tattcgaactccgttgctgttg-------tctgtacctctgttgcagaagata-aatcaaatttatttttgccatccactag
||||| ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||| || |||||||||| | ||   | ||   ||||  ||  | |||       || ||   | | |    | |  || |||||  ||| |  |||||| |   |||
TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtatattctttctactctatttttattggcaaggttcagttattgtctccttggaactataatcagttttctggttgccaacttttag
















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|58595654|gb|CK006182.1|CK006182
EST:     CTTTCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG                         GGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCT
genomic: CTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattac ... catccactagGGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCT
EST: gi|58683626|gb|CK072313.1|CK072313
EST:     CTTTCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG                         GGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCT
genomic: CTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattac ... catccactagGGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCT
EST: gi|163918501|gb|EG711431.1|EG711431
EST:     CTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG                         GGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCT
genomic: CTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattac ... catccactagGGCTGTACATTTGTTCCACCTACTGTCCGGTCAAAAGCTGGAGTGCTCCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAGgtaaaattactattcgaactccgttgctgttgtctgtacctctgttgcagaagataaatcaaatttatttttgccatccactag

- - - - - - - - - - - GCAAGA
- - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - -  AGAAGT