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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG

Basic information

species Oryza sativa
transcript LOC_Os05g16660.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 5
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttctt-ttgcaatgttattttttcg--tttagcaataagacacttatattttactttc----agATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
|| | ||||||       |||  ||  |||   |  ||  |  ||     | ||||   || |||  |    || |||  || |   ||| | | |       ||| |  || || ||    |||||||||||||||||||||||||||| ||||| |||||||| |||||||| ||  ||||||||||||||||||| |||||
gtaatttcttttt---cagttaataaatta---tcaaggcattactccttttgtgttacttccttgctaacttggtatacttacaatttttgaactgttctgattaaaacttgctctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 5
-------gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
        |||||||   | | ||   | |  |  | | |||  || | | |  || ||   | |  | |||     |   |||||   |  |||  | ||| ||       ||   |||| |||||||||||||||||||||||||||| ||||| |||||||| |||||||| ||  ||||||||||||||||||| |||||
gtgatttttcagttcacagaatataaatgccttactctttttgtgttacatct-tgctaactttgcatgctt-----acaatatttgaaccattattattaaaac-------ttgctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G36870.2 (Glycine max), 3'ss of exon 3
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgta-gttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG----
                            || |||||  |        | ||| | || |||   || || |||| ||||   | || ||   ||    |  || ||||| |   | ||||| | ||||| |||||||| ||||| |||||||| |||||||||||||| ||| |||| ||||| |||||||||   ||    
---------------------------gtaggtttttttttccttcct-atactatatgttgagttctgtaatggtattgaat-gtctacttatttcgcttttttatttca---ttagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTAT

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 6
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactt--tcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
    ||| |||     |  || || |  |||||||   |      ||||||| ||||   |    ||   || ||  |||||  || |          | || |  || | ||  | ||||| | ||||| |||||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| |||||||||   ||
----gtttttttttttt--ttcctttactatgtttagttctc--taatgata-tgtaacatctactt---attttgctttttatttca---------tatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 3
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
|| ||||  ||     || |||   || ||   | |  || | ||  ||||  | | |  |   |    | | |  ||  ||  |||             ||  |||| | |   ||||| | ||||| |||||||| ||||| ||||||||||||||||||||||| ||| |||| ||||| |||||||||   ||
gtaagtttgtt-----tgcttttcttcctagactatgttgtgtactgtgatgatattgaatgtctacttattttgcttccttttttt-------------tttcatttgatt---agATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 3
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgta-gttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
                            || |||||  |        | ||| | || |||   || || |||| ||||   | || ||   ||    |  || ||||| |   | ||||| | ||||| |||||||| ||||| |||||||| |||||||||||||| ||| |||| ||||| |||||||||   ||
---------------------------gtaggtttttttttccttcct-atactatatgttgagttctgtaatggtattgaat-gtctacttatttcgcttttttatttca---ttagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactt--tcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
|| |||| |||     |  || || |  |||||||   |      ||||||| ||||   |    ||   || ||  |||||  || |          | || |  || | ||  | ||||| | ||||| |||||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| |||||||||   ||
gtaagtttttttttttt--ttcctttactatgtttagttctc--taatgata-tgtaacatctactt---attttgctttttatttca---------tatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacact-tatattttacttt--------cagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
                                     || ||        ||    |||||| |||   ||  || |    | |   ||  ||| |  ||| | |||||    ||         ||||| ||||||||||||||||||| || ||||| ||||||||||| ||||| ||  ||||||| | |||||||||   |||
-------------------------------------gttagtgttgcagtaaaacagttttatttaaaaac-ttgtaacctggaa-agagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
gtcagttctttgcacatggtttctatctta-tgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
           |    || ||   ||   | ||||||| |  |||  ||| ||   | |      |   ||   |||  |   ||| || || |  |     |||| | ||     ||||| |||||||||||||||||||||| ||||| ||||||||||| || || ||  ||||||| |||||||||||   |||
-----------gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaaa--tacacatatttaaataaccgtgtatcattgtgtttggtataatatat----agATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

upper sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactt-tcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
                    | |  | |||   ||||      | | | ||     | |     |    ||   ||         |    | | |    ||  |  || || |  ||||||||  ||||||||||||||||||| || |||||||||||||| ||||| || || |  ||||||||||| ||| ||||
------------------aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG

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|86495724|gb|CI138357.1|CI138357
EST:     CTATGACAGATCGTCGAGCGGGAAAATTTGAAGCGAAATTCTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGAGCGGGAAAATTTGAAGCGAAATTCTTTCACAAGgtcagttctt ... ttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAAC
EST: gi|55411136|gb|CV723512.1|CV723512
EST:     CTATGACAGATCGTCGAGCGGGAAAATTTGAAGCGAAATTCTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGT
genomic: CTATGACAGATCGTCGAGCGGGAAAATTTGAAGCGAAATTCTTTCACAAGgtcagttctt ... ttactttcagATTTTGCAAGAGGAAATTGGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG
                                           ttttactttc  CT-rich tract
                                    acttatattttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA