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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA

Basic information

species Oryza sativa
transcript LOC_Os02g44510.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 4
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA
                                                                                   |||| ||    || |||||||||| | |||| |    | ||| | || || || ||||||||    |||    |||||||||||||||| || ||||| | |||||||| ||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||||||||  | |
---------------------------------------------------------------------------------gtatatgag----ctacctttgagtttattaatcacttaagattgggtgtctattttctaacca----tcccgctgccagGATGTCATACCGCACATGGCTCGGGAATATGAATTCGAGTATGAGCTCGTCACATATAAATGGCCAACATGGTTACACAAGCAGAAAGAGAAGCAAAGGA

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 32
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgcctttagttgagtattt-catgagaagatattag-atgtcttcctttga-gttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA
                                              ||| || ||  ||   ||||   |  || |||   ||   ||| | || |     | | | || || | |||||      | | ||  |||     |      | |   ||    |||||  | || || || |||||||  || ||||| ||||| || || || ||||| || || ||||| ||||||||||| || |||||||| ||||||||||
---------------------------------------------gttatatatccaccca-agttatatgcttacattttaattcatttgtatattggaatgtaaagtagaatgatgagtttgcctgacat-tctgaaccattttggttgacttaacatacagGACTTAATTCCACACATGGCCCTAGAGTATGGTTTTGAATATGAACTAGTCACGTACAAGTGGCCCACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 34
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgc-ctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA
                       |||   |||  |   |       ||| |||  | |  |||| || | ||| |  ||  |     ||| |||      ||  ||| || | |||||      | | || ||||   | |      | |   ||    |||||  | || || || |||||||  || ||||| ||||| || || || |||||||| || ||||| ||||||||||| || |||||||| ||||||||||
-----------------------gttatatatccacccaag-----ttatatgcttacattttaattcattatatattggaa---cgttaaatgg-----ttaaagtagaatgatgagtttgcctgacat-cctgaactgttttggttgacttaacatacagGACTTGATTCCACACATGGCCCTAGAGTATGGTTTTGAATATGAACTAGTCACATACAAGTGGCCCACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 31
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatat-tagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA
                       |||    ||  |   || | ||   |  |||| |   || | |||  ||||  |     | |  |   || |  |   ||   |  | |     |||  ||||   ||| |||||||| | |||            |||||| | || || || ||||| || |||||||| ||||| | ||| ||  |||| || |||||||| ||||||||||| || |||||||| ||||||||||
-----------------------gttatacatccacacagtatatgcctcaatgttta--ttcatttgtatattggaactttaaa-gtggaatataatgagtttgctcaacttcctcgaac-tatt--ttgcttgttgtcttaacaaa-----------cagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtcta--accaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA
                                            |   |    | | | || | |    | |||  ||    ||   | | ||| ||| | | | || | |   |  ||  | |||   |     | |||        |||         |||||||| || || |||||||| ||||||||||| |||||||| ||| |  | || || |||||||||||||||||||| || |||||||| ||||||||||
-------------------------------------------gttgcaaccattttctttcactcttct-tttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

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|58658861|gb|CK047541.1|CK047541
EST:     GACCTGTGAAATTCTGGTTCATAAAGAACTATCTATCTCCACAGTTCAAG                         GATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
genomic: GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAGgtacgtgagc ... caatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
EST: gi|58609426|gb|CK037459.1|CK037459
EST:     GACCTGTGAAATTCTGGTTCATAAAGAACTATCTATCTCCACAGTTCAAG                         GATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
genomic: GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAGgtacgtgagc ... caatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
EST: gi|29624544|gb|CB629555.1|CB629555
EST:     GACCTGTGAAATTCTGGTTCATAAAGAACTATCTATCTCCACAGTTCAAG                         GATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
genomic: GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAGgtacgtgagc ... caatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
EST: gi|33794022|gb|CF322901.1|CF322901
EST:     GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAG                         GATGTCATACCCCATATGGCCCAGGAATATGGATNTGAGTACGAGCTTGTC
genomic: GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAGgtacgtgagc ... caatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
EST: gi|58689586|gb|CK078273.1|CK078273
EST:     GACCTGTGAAATTCTGGTTCATAAAGAACTATCTATCTCCACAGTTCAAG                         GATGTCATACCCCATATGGCCCAGGAATATGGATTCGAGTACGAGCTTGTC
genomic: GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAGgtacgtgagc ... caatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
EST: gi|58658473|gb|CK047153.1|CK047153
EST:     GACCTGTGAAATTCTGGTTCATAAAGAACTATCTATCTCCACAGTTCAAG                         GATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC
genomic: GACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTCAAGgtacgtgagc ... caatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA
                              gtctaac  putative branch site (score: 2)
           aagatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC