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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT

Basic information

species Oryza sativa
transcript LOC_Os03g43930.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 6
gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactat-attctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
|||||   ||||  ||||||         | || |  |    | |||||||| |  | | | |     |  ||| || || |  ||| ||||||| ||||| ||||||||||| || ||||||||||| |||||||| ||||||||||| || ||||||||||| || ||||| |||||||||||||
gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccagcctcacagcattgtattatcctttggcagTTGTGCAGTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G423337_T03 (Zea mays), 3'ss of exon 3
gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactat-attctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT--------
|||||   ||||  ||||||         | || |  |    | |||||||| |  | | | |     |  ||| || || |  ||| ||||||| ||||| ||||||||||| || ||||||||||| |||||||| ||||||||||| || ||||||||||| || ||||| |||||||||||||        
gtatacgatcagctagcattttcactttgtcttcttttcagctgtgttgttgcaccagcctcacagcattgtattatcctttggcagttgtgcagTGGTGTGGATGAAAATGCAGCTGGTGCATGTGCACAGCTTGTGTTTGCACCCATCGATGAATCTTTTGCCGACGATGCGCCACTGCTACCCTCAGGCTTC

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 13
---------------------------------gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
                                 |   || ||     |||| ||    | || | || |  | |||  | | ||   ||| |||  |    | | || |  | |  ||||||||||| ||  | |||||||||||    || || ||||| |||||||| |||||||| ||||| ||||| ||||| |||||||| |   | || || |
gtaaagttatttttgtgttcgggttgttggtctgctcatcttatttaagcagtaactagtaactgttactgtgaat--gatttttatttaccttatta---tgcaatttgatgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATTGGAGCGTGTGCACAGCTTGTGTTTGCACCTATTGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 13
-------------------------gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
                         | |||||||  |     | |||   || ||   |   |||  | ||   || ||| | |||  ||   | | |  |  | |  ||||||||||| || || |||||||||||    || |||||||| || ||||| |||||||| ||||| || || |||||||||||||| |   |||| || |
gtattgtgtgtgactttttggctttgcatattttatgta---actaggaagctatagctattttctgtgtgacatttgatgacctt--tgctatgcgacttgatgtggcagCTGTGCAGTGGAGTTGATGAAAATGCAATTGGGGCATGTGCTCAACTTGTGTTTGCACCTATTGATGAGTCCTTTGCTGATGATGCTCTGTTGCTTCCAT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 13
---------------------------gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
                           | |||| ||   | |  | |||   || ||   |   ||   | ||    | ||| | | |  ||   |      |  | |  ||||||||||| || || ||||||| ||| |  || |||||||| || ||||| |||||||| ||||| || || |||||||||||||| |   | || || |
gtagtgtgtgtgaatttattaccgtttgcatatctt---atataactaggaagctatagctattttgtgtgtgacacttgatgacccttttgttatgtgtcttgatgtgacagCTGTGCAGTGGAGTTGATGAAAGTGCAGTTGGGGCATGTGCTCAACTTGTGTTTGCACCTATTGATGAGTCATTTGCTGATGATGCTCTGTTACTGCCAT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 13
-------------------------------gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
                               ||   |||||  |    ||||  |    |  |  | | |     || | ||   || || | || |  | | || |  | |  ||||||||||| ||  | |||||||||||    || |||||||| |||||||| |||||||| || || ||||| ||||| |||||||| |   | || || |
gtaaagtcatttttgtgtttgtgtttaggttgttggttttcttatcttattaaagcaggaactagttactgtgaatgatttt---tttaccttatta--tgcaatttggtgtggcagCTGTGCAGTGGAATTGATGAAAATGCAATCGGAGCATGTGCACAGCTTGTGTTTGCACCTATCGATGAATCATTTGCAGATGATGCTCTCTTACTGCCTT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatt--tcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
|| |  |||     |     | |  |  ||| ||  |    |  | |||    ||| | ||  ||   |  | | | || ||   ||||| || ||||| || ||||||||||  |  || |  ||||| |||||||||||||| || || || ||||| |||||||||||||||||  |||| || |
gtttgctttatactaaagacactcagggattcttaaagatgagttattg--aaattgaattcttggtttcttttttgcttttgtccagCTTTGTAGCGGCGTTGATGAAAATGTGGTTGGAGGTTGTGCTCAGCTTGTCTTTGCCCCAATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
|| |   |||| |   | |||      || ||| |       | |||| |     | || |  || | | ||  |||||  |  |||| || |||||||| ||||||||||  |  || |  ||||| |||||||| ||||| || || || ||||| |||||||||||||||||  |||| || |
gtttgacttcata---ctttaactccaaagtttctatgctcctttgttctcttcatgacattttg-gattcttgattcttgtctagCTTTGTAGCGGTGTTGATGAAAATGTGGTTGGAGGTTGTGCACAGCTTGTATTTGCCCCTATCGATGAATCATTTGCTGATGATGCACCTTTGCTTCCTT

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 13
---------------gtatattttca-gagagcattagtgtgcaattttttcatt--caatctgttgttggattaacttgatgaggta-------ct---atattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
                || || || | | |||   |  ||   |  ||||||||    |     ||||  | ||| |||  |||  ||       ||   || |||| |  ||||| ||||| || || ||||| ||||| || ||||| ||||| ||||| || |||||||| ||||| ||||| |||||||||||||| ||  |||| || |
gttggtttgtctataataaatatttatgggagtgattttgcttatctttttcataggtagaactttgtaagtttatcttattgacataaatatttcttaaattttctgtggcagCTATGCAGTGGGGTTGATGAGAATGCAGCTGGTGCCTGTGCTCAGCTGGTTTTTGCACCTATTGATGAATCATTTGCTGATGATGCTCCTTTGCTGCCAT

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|88362295|gb|CI608686.1|CI608686
EST:     GCCTCTGCCATGATGAGGTCGTTCTATCAAGAGATATGTACCTTCTGCAG                         CTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTC
genomic: GCCTCTGCCATGATGAGGTCGTTCTATCAAGAGATATGTACCTTCTGCAGgtatattttc ... tctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT
                                            ttctatttc  CT-rich tract
                                     tactatattctattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttcagagagcattagtgtgcaattttttcattcaatctgttgttggattaacttgatgaggtactatattctatttcagCTGTGCAGCGGTGTAGATGAAAATGCTGCGGGTGCATGTGCCCAGCTTGTCTTTGCACCCATTGACGAATCTTTTGCTGATGATGCACCACTGCTACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT