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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaaatctagtttgtgtaaataacaatttacatccagtgattgtattttgnatatttttgttgtag

Basic information

species Oryza sativa
transcript LOC_Os04g45970.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G427097_T01 (Zea mays), 5'ss of exon 4
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgt-atactatacaacaacacaaatctagtttgtgtaaataacaatttacatccagtg--attgtattttgnatatttttgttgtag--------------------------------------
|||||||| |||||  ||||||||||||||||||| |||||||| || || ||||| |||||||||||||||||||||||| | |  ||    || |  || |  | || |||  |||||   |||  |   |||   ||   |      | || |      |||                                      
ACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAgtaagtgaaaaaatgtggcagc--aagttaaattggtgccaataaacttttttacaaagtataatataacagaaaaaatgtacacaatagttattatcatttttactcttttttgtttgttgttgtag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G41310.1 (Glycine max), 5'ss of exon 4
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaaatctagtttgtgta---aataacaatttacatccagtgattgt----attttgnatattttt-gttgtag-----
|| |||||||||||| | |||||||| || || || ||||| |||||||| |||||||| |||||||| || |||||||||||| | | ||  | ||    |     |||| ||   ||| | || |||  |  ||  |||||    |||||  | |||||| ||||| |     
ACAATGGCTTGGATTCTTGATGAGTATTCTAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAACCTATAgtaagtataatgtgcataatcatcctttgttcttgtatacacaatcataacttatttgtagaaattgttttaattttcaacattttttgttgtggtgtag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G07440.1 (Arabidopsis thaliana), 5'ss of exon 3
-------------------------ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatacta----tacaacaacacaaatctagtttgtgtaaataacaatttacatccagtgattgtatt---ttgnatatttttgttgtag-----------------------------------------------------------------
                         ||||||||||||||| | ||||||||||| || || ||||||||||| || || ||||||||||| ||||| || |||||  |  ||    |      | |  | |||   |   | |  |     ||    |   |   || | ||   ||| ||   || | |||                                                                   
TCCTGATATGGGCACTAACGCTCAAACCATGGCTTGGATTCTTGATGAGTACTCCAAGTTTCATGGTCATTCCCCTGCTGTTGTCACTGGAAAGCCCATTgtaaggcttttaagattttggttatatcattctgagtccggaatctgttgtttattctatggatgttttcttgatttgaattaattcgatgtttctatgtgattaccatagttttgagctttttggtatagaagtaactgttggatcactttggtgtag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0039g02720.t01 (Vitis vinifera), 5'ss of exon 4
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaa--atcta--gtttg--tgtaaataacaatttacatccagtgattgtattt-tgnatatt-tttgttgtag-----------------------------
|| ||||| |||||||| || |||||||| |||||||||||||| |||||||| || || ||||| |||||||||||||||||     |||| ||  | |  |||||   |||   | |   |||   |||  |       |  | |||| |   | || ||| ||||                               
ACTATGGCATGGATTTTCGACGAGTACTCAAAATTCCATGGTCACTCACCGGCTGTAGTGACTGGAAAGCCAATAgtaagtatttgcgacaaaaaaccgagcatctatgatttagatttgtgtaaacctttgaagttgagaaacgaatttgtaactgttgtttcttgttctgtggcctcatttacatttgggcttttag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0039g02750.t01 (Vitis vinifera), 5'ss of exon 4
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaa--atcta--------gtttgtgtaaa---taacaatttacatccagtgattgtattttgnatatttttgttgtag-------------------------
|| ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || ||||| |||||||||||||||||     |||| ||  | |  |||||         ||||||||||   |   | |  | |  ||    |||||  |    | | ||  |  | |                         
ACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATAgtaagtatttgcgacaaaaaaccgagcatctatgatttagatttgtgtaaacctttgaagtcgagaaacaaaatttgtaactgttgtttcttgttctttggactcatttacatttgggcttttag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S62_236V6.1 (Physcomitrella patens), 5'ss of exon 5
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgta---------tactataca------acaacacaaat-ctagtt----tgtgtaaataacaatttacatccagtgattgtattttgnatatttttgttgtag--
|| ||||||||||||||||| |||||||||||||| |||||  || | ||||| || || ||||| || ||  | ||||||          ||| | | |      ||| |  ||   || |||    ||| | ||| || ||     |||   |||||    ||   | ||  | |  |    
ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTGgtaagttaatgtctcctaccaaaaactgtgtacagcttaaccgcttgttcagatgtttgaatgactatccctttcctacgattgatccttttcttttactttcatgaag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaaatctagtttgtgtaaataacaatttacatccagtgattgtattttgnatatttttgttgtag
||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| | |||||  |  | |     |  |  | | |  |||||        |   | | ||   ||  |||  | |                  
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatca-tttgatttgt--------cctctgatatt--gtttttgcttctcag---------------

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ36430 (Selaginella moellendorffii), 5'ss of exon 4
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaaatctagtttgtgtaaataacaatttacatccagtgattgtattttgnatatttttgttgtag
||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| | |||||  |  | | |           |   | || | | | |     | |  ||   ||  |||  | |                  
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttct----------ttctgattatttgatttgtcctctg-atattgtttttgcttctcag---------------

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|29678534|gb|CB674809.1|CB674809
EST:     GAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAG-A-                         -TCTTGGTGGATCATTAGGTAGAGATGCTGCTACAGGAAGAGGTGTGATGT
genomic: GAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactata ... tttgttgtagGTCTTGGTGGATCATTAGGTAGAGATGCTGCTACAGGAAGAGGTGTGATGT