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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgccactagattgatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
----------gtaatgccactagatt--gatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaa-cattgtccatatttcc--agGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
           | |   || || ||   |||   | |   |||     ||| |  ||     ||| | |  |    ||  | ||| |||| ||| |  ||||||| ||||||||||| |||||||| |||||||||||| |  ||||||||||||||||| |||||||| | ||
acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
gtaatgccactagattgatcatgattgctaccgttttatgtccatc-----ttattggctaaaa---agtgacaaca-------ttgtccatatttcc--agGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
    |   |  |  ||  |    ||  |  ||  |  ||||  ||      | |  |   |||     |||  ||||       ||| |||| ||| |  ||||||| ||||||||||| |||||||||||||||||||||||| ||||||||||||||||| |||||||||| ||
--cttcttaagaatttttttccaatctcatccaatccatgtgtattgggaataaccgaacaaagcctggtgtgaacactattctttgcccatgttttctcagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
gtaatgc--cactagattgatcatgattgct-accgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttcc--agGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
||||||    || ||||||||||  |||  | ||   |||   | || | || ||| ||  ||       | ||| |||| ||| |  ||||||| ||||| ||||| |||||||||||||||||||||||| ||||||||||||||||| |||||||||| ||
gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
--------gtaatgccactagattgatca--tgattgctaccgttttatg---tccatcttattg--gctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
         | |  ||     |  |||    | ||||||  | |  |||    |  |  |||||   | ||  |    ||   | | |  |    |  |||| ||||| |||||||||||||||||||||||||||||||| || |||||| | | |||  || |||| |    
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
------------gtaatgccactagat-tgatcatgattgctaccgttttatgtccatcttattg--gctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
              |  |  |  |||| |  ||||   |       | |||     |  |||||   | ||  |    ||   | | | ||    |  |||| ||||| |||||||| ||||||||||| ||||||||||| || |||||| ||| |||  || |||| |    
tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaatgccactag--attgatcatgattgctaccgttttatgtccatcttattggctaaa-aagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
||| | |   ||   ||| ||      |||||||   || | |   | |   ||| |  |  | |    | |||| |  |||   |||||||| ||||| |||||||| ||||||||||| || ||||| || |||||| ||| |||  || | |||||  |
gtactacttatactcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattg-ctgtat---cagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------------------------gtaatgccactagattgatcatgattgctaccgttttatgtccatctt--------attggctaaaaagtgacaacattgtccatatttc----cagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
                                                    ||  |||| | |     | |   |||||  |  |||||    ||||        |||   ||   | |  | |    |   ||   |     ||||| || ||||| ||||| |||||||||||||||||||| ||  |||||||||||| |||  || | |||||  |
gtagtatctctatccttcgtttaccatggtgatccttcaatattccaccaacaactccacaacaccttacctacatgctaggggcttatgaatctcttgcgaatcaattttttatttacttgcgaatccgatgatggcttgttacagGTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
------gtaatgcc-actagattgat-catgattgctaccgttttatgtccatcttattggctaaaaagtgacaac-------attgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
         ||||| |||||| |  |  |  ||       |  ||  ||    | | | |  | || |||||           |||    | | ||  |||| |||||||||||||| ||||| |||||||||||||| ||  |||||||||| ||||| |||   ||||| ||
ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------gtaat-gccactagattgatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
                               ||| | |||   |     |  |  ||| |     ||||     ||| ||   | || |   |||       ||| |   |   |||||||| ||||| ||||||||||| ||||||||||| || || |||||  |  |||  || ||    |||     
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaag--aaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcg---tgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------------------------------------------------------------gtaatgccactagattgatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttc-----cagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
                                                                               || ||| |    || ||| |||    |  || |||      |     |||    | |         || |||| ||      ||||| |||||||||||||| ||||| |||||||| ||||||||  ||||  | |||| |||  |    |||     
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcgg--aataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA

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|163929405|gb|EG713830.1|EG713830
EST:     TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG                         GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAGgtaatgccac ... atatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
EST: gi|86504183|gb|CI146816.1|CI146816
EST:     TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG                         GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAGgtaatgccac ... atatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
EST: gi|86500499|gb|CI143132.1|CI143132
EST:     TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCGTCACTGAGCTTGGCAAG                         GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAGgtaatgccac ... atatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
EST: gi|86480028|gb|CI122661.1|CI122661
EST:     TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG                         GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC
genomic: TCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAGgtaatgccac ... atatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
                     ggctaaa  putative branch site (score: 3)
                                              tatttcc  putative PPT
             atcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgccactagattgatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC