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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCACTGTGGGAAAGTCTCCTGCTCACAATGATGGTGCAGGAACTTTGGGTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgttctcttaccctgttgttcaactttaagttatttaaatctggccaggccatccagaaattttatgttcccctttctattttcag

Basic information

species Oryza sativa
transcript LOC_Os12g44330.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G147811_T01 (Zea mays), 5'ss of exon 4
CTTCACTGTGGGAAAGTCTCCTGCTCACAATGATG---------GTGCAGGAACTTTGGGTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgttctcttaccctgttgttcaactttaagttatttaaatctggccaggccatccagaaattttatgttcccctttctattttcag
         ||||| |||||||||||||||| |||         |  | ||| | ||   | || |||| ||||  |||||||||||||||||||||||  |||| ||||||||| | | ||  || | | |   ||||  | ||  ||||  |||     ||   ||||| ||||  |||     ||| |||   || |||
---------GGGAAGGTCTCCTGCTCACAATTATGCTTCAACTAGCACGGGAGCATTCACTGATGAGAGGACAATAGGTGTTTCAGGTCTTGGAGAGGGTTCTCCCAAGgtaattgtttcctgctatcgtat---tcaa--tgaacatatt--aatt----catatcatcctgaaaacttactagtccccttcgtattccag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G151236_T03 (Zea mays), 5'ss of exon 4
CTTCACTGTGGGAAAGTCTCCTGCTCACAATGATG---------GTGCAGGAACTTTGGGTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgttctcttaccctgttgttcaactttaagttatttaaatctggccaggccatccagaaattttatgttcccctttctattttcag------------------
         |||||||||||||||||| ||||||          |  | ||| | ||   | || |||| ||||  | |||||||||||||||||||||  |||| ||||||||| | | || |||         || | || ||  ||   | ||     ||   ||||| ||||  |||    || | |||   || |||                  
---------GGGAAAGTCTCCTGCTCAAAATGATACTTCAACTAGCACGGGAGCATTCACTGATGAGAGGACAATAGATGTTTCAGGTCTTGGAGAGGGTTCTCCCAAGgtaattgtttcctgtta---------tcgaattcaa--taaacatattaattcatatcatcccgaaaacttactagcctccttcatattccagagtgagagatcagcagac
















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|33690079|gb|CF318318.1|CF318318
EST:     GTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAGG                         AGTGAGAGATCGGCGGATATGTTTTGTGATGACATTTTTGGAGAATCACCT
genomic: GTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgt ... ctattttcagAGTGAGAGATCGGCGGATATGTTTTGTGATGACATTTTTGGAGAATCACCT
EST: gi|218495214|gb|FG943438.1|FG943438
EST:     GTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAG                         AGTGAGAGATCGGCGGATATGTTTTGTGATGACATTTTTGGAGAATCACCT
genomic: GTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgt ... ctattttcagAGTGAGAGATCGGCGGATATGTTTTGTGATGACATTTTTGGAGAATCACCT
EST: gi|87016978|gb|CI286114.1|CI286114
EST:     GTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAG                         AGTGAGAGATCGGCGGATATGTTTTGTGATGACATTTTTGGAGAATCACCT
genomic: GTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgt ... ctattttcagAGTGAGAGATCGGCGGATATGTTTTGTGATGACATTTTTGGAGAATCACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCACTGTGGGAAAGTCTCCTGCTCACAATGATGGTGCAGGAACTTTGGGTAATCAGAGAACAACTGGTGTTTCAGGTCTTGGAGAGGGCACTCCAAAGgtaattctgttctcttaccctgttgttcaactttaagttatttaaatctggccaggccatccagaaattttatgttcccctttctattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG