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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctccagtgttctagatcagcacaatt...

Basic information

species Oryza sativa
transcript LOC_Os07g06440.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G455171_T01 (Zea mays), 5'ss of exon 13
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctccagtgttctagatcagcacaatt-----
| |||||||| |||||||||||||||||  |||| || |||||||||||| | ||||||||||||||||||| ||| ||  || || ||||| || | |||||  |   ||| ||||| ||     ||  | ||       | | |     |||  |  |||    ||||  |     |      |  |    |||         
AACAATTTGAGTTGGCTGAAGCAGTAAAGCTGCCCATTTTTCTTCACATGTGTGCTGCTGGTGAAGACTTCTATGAAATCATGACACAAAATTTGCACAGgtagcatataatttgtattccg----taggt-ggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactggccgtag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G081668_T01 (Zea mays), 5'ss of exon 2
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtatacca---atactatataggcaaggagcc-------aaggactactga----ggagtactgctttgtactcctccagtgttctagatcagcacaatt---------------------------------------------------------------
| |||||||| |||||||||||||||||| |||| ||||||||||||||| | |||| |||||||||||| ||||| ||  || ||   ||| || | |||||  |   ||||||||| ||     |  | |      | |  |||       |   |||| ||        | |    ||   | | | |  ||  |     | | | |  ||                                                               
AACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGTGTGCTGTTGGTGAAGACTTATGTGAAATCATGACACGGAATTTGCACAGgtagcatataatctgtattccgtaggtggtgttcctcaatgatgccctgctggatacactattgtttttaatgaaacagttgaaagtacactggtcgtaggagttacctctgtttcaattcacttgttatgtttataactattccttgatctctgtgtctgtttttctctttggcag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G081668_T02 (Zea mays), 5'ss of exon 9
-AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgagga-gtactgctttgtactcctccagt-----gttctagatcagcacaatt---------------------------------------------------------------------------
 | |||||||| |||||||||||||||||  |||| || |||||||||||| | ||||||||||||||||||| ||| ||  || || ||||| || | |||||  |   ||||||||| ||       |   |      |   | |  || |||   |    ||  ||| || |    ||||     || |     | | |  |||                                                                           
AAACAATTTGAGTTGGCTGAAGCAGTAAAGCTGCCCAT-TTTCTTCACATGTGTGCTGCTGGTGAAGACTTCTATGAAATCATGACACAAAATTTGCACAGgtagcatataatctgtattccgtag--gtggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactggccgtaggatttacctatgtttcaattcacttgttatgttttataactattcattgatctttgtgtctgttttttctctttggcag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G095969_T01 (Zea mays), 5'ss of exon 7
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctccagtgttctagatcagcacaatt----------------------------------------------------------------------------------
| |||||||| |||||||||||||||||| |||| ||||||||||||||||| ||||||||||||||||||||||| ||  || ||   ||| || | |||||  |   |||||||||  |  ||   |   |      |   | |  || ||| |    ||| |||  |  |  |  |    |  | |  |      ||                                                                                  
AACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGGAATTTGCACAGgtagcatataatctgtat-tcggtag-gtggtgttcctcaatgatgccctgctg-gatacact-cttgtttttaatgaaacagttgaaagtacactggttgtaggagttacctatgtttcaattcacttgttatgttttataactatttcttgatctctctgtctgtttttctctttggcag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G894029_T01 (Zea mays), 5'ss of exon 19
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcc-tccagtgttctagatcagcacaatt----
| |||||||| |||||| |||| |||||| |||| ||||||||||||||||| |||| |||||||||||| ||||| ||  || ||  |||| || | |||||  |   ||||||||| ||     ||  | ||       | | |     |||  |  |||    ||||  |   |  |    |  | |  |      |     
AACAATTTGAGTTGGCTAAAGCTGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGTTGGTGAAGACTTATGTGAAATCATGACACGAAATTTGCACAGgtagcatataatctgtattccg----taggt-ggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacattggtcgtag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G051032_T01 (Zea mays), 5'ss of exon 9
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctccagtgttctagatcagcacaatt-----------------------------------------------------------------------------------
| |||||||| ||| |||||||||||||| |||| ||||||||||||||||| ||||||||||||||||||||||| ||  || || | ||| || | |||||  |   ||||| ||| ||     ||  | ||       | | |     |||  |  |||    ||||  |     |      |  |    |||                                                                                       
AACAATTTGAGTTGTCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACAGAATTTGCACAGgtagcatataatctatattccg----taggt-ggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactggccgtaggagttacctatgtttcaattcacttgttatgttttataactattccttgatctctgtgtctgtttttctctttggcag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G455171_T01 (Zea mays), 5'ss of exon 17
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctccagtgttctagatcagcacaatt----------------------------------------------------------------------------------
| |||||||| |||||||||||||||||| |||| ||||||||||||||||| |||| |||||||||||| ||||| ||  || || | ||| || | |||||  |   ||||||||| ||     ||  | ||       | | |     |||  |  |||    ||||  |     |      |  |    |||  |                                                                                   
AACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGTTGGTGAAGACTTATGTGAAATCATGACACAGAATTTGCACAGgtagcatataatctgtattccg----taggt-ggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactgtcgtaggagttacctctgtttcaattcacctgttatgttttataactattccttgatctctgtgtctgtttttctctttggcag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G704381_T01 (Zea mays), 5'ss of exon 2
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcc-tccagtgttctagatcagcacaatt----------------------------------------------------------------------------------
| |||||||| ||||||||||||||||||  ||| ||||||||||||||||| |||||||||||| |||| ||||| ||  || ||   ||| || | |||||  |   ||| ||||| |      ||  | ||       | | |     |||  |  |||    ||||  |   |  | |  |  | |  |                                                                                          
AACAATTTGAGTTGGCTGAAGCAGTAAAACAGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAAACTTATGTGAAATCATGACACGGAATTTGCACAGgtagcatataatatgtattctg----taggt-ggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaatagttgaaagtacactggccgtaagagttacctatgtttcaattcacttgttatgttttataactattccttgatctctgtgtctgtttttctctttggcag

upper sequence: LOC_Os07g06440.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G52390.2 (Arabidopsis thaliana), 5'ss of exon 8
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctcc-agtgttctagatcagcacaatt
||||||||||| | ||  | ||   ||| ||||||||||| || |||||||| || |||| |||||| |||||||| |||||      |||   | |||||| |      |  || |  | |||  | | | |     | |   ||    |||     |      ||| || || ||  | |    |   |||     |  
AGCAATTTGAACTAGCATATGCTACAAAGTTGCCAATGTTCCTACACATGCGAGCAGCTGCTGAAGATTTCTGTGAAATTGTTGAGAGAAACAAGAATAGgtga------acatgcaggctaatgatttttcga-gttgtgtttagataaacttcctggattgattttttagtcatcttaatcccatgattcactttcag-

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|27334380|gb|CA882831.1|CA882831
EST:     CGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAG                         ATTCCCTGGGGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGA
genomic: CGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactca ... tccatcgcagATTCCCTGGGGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGA
EST: gi|58695600|gb|CK084287.1|CK084287
EST:     CGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAG                         ATTCCCTGGGGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGA
genomic: CGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactca ... tccatcgcagATTCCCTGGGGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAAAATCTGTATAGgtaatactcaatctgtataccaatactatataggcaaggagccaaggactactgaggagtactgctttgtactcctccagtgttctagatcagcacaatt

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc