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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacag

Basic information

species Oryza sativa
transcript LOC_Os01g60700.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60700.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068151_T01 (Zea mays), 5'ss of exon 3
AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacag
|||||| |||||||||||||||||||||||   ||||||||||||||| || |||||||| ||||| || |||||| | ||||||||||| || |||||||| |    | |||     ||  ||| ||   |||      |  | ||    |    |  |     | || |||    |  | ||  ||   | |||||  |||| | |   |||  | | | |            
AAGATCAGATGGTCGTTTCATGGACTGGTCTAAACGTTTGAAGGTTGCCCTGGGTGCTGCCAGAGGTCTAGCTTTCTTGCATGATGAAGGACCCTTTCAGgtgatca-tgcta----cttgatttatggtcttatgggctatggcat-cacacaaaaggtgtgcttttaatac-cgagccgctgactt---aacttgta-tttatatttccatttgtttttcag-----------

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G079117_T01 (Zea mays), 5'ss of exon 1
AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttac--tgcttctaaactttttctttt-tgacattac-caataagtgaatattta-----ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacag
|||||| |||||||||||||||||||||||   ||||||||||||||| || |||||||| ||||| || |||||| | ||||||||||| || |||||||| |   |||| ||  | || |  | || || ||| || ||| | |||    ||||     |||||  | |   |  |  |||||   | ||  |      ||  |  |  | ||||  |||| |||| |  ||||  ||| |||
AAGATCAGATGGTCGTTTCATGGACTGGTCTAAACGTTTGAAGGTTGCCCTGGGTGCTGCCAGAGGTCTAGCTTTCTTGCATGATGAAGGACCCTTTCAGgtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttttatttggcattcaaccacattatcttataataccgagcc--gctgacttaacttgtatttatatttccatttggttttcag

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G143790_T01 (Zea mays), 5'ss of exon 1
AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttac--tgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacag
|||||| ||||||| |||||||||||||||   ||||||||||||||| || |||||||| ||||| || |||||| | ||||||||||| || |||||||| |   |||| ||  | || |  | || || ||| || ||| | |||    ||||   |||||  | |   |  |  |||||   | ||  |      ||  |  |  | ||||  |||| |||| |  |||| |||| |||
AAGATCAGATGGTCATTTCATGGACTGGTCTAAACGTTTGAAGGTTGCCCTGGGTGCTGCCAGAGGTCTAGCTTTCTTGCATGATGAAGGACCCTTTCAGgtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataataccgagcc--gctgacttaacttgtatttatatttccatttgtttttcag

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G828466_T01 (Zea mays), 5'ss of exon 1
AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttac--tgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacag
|||||| |||||||||||||||||||||||   ||||||||||||||| || |||||||| ||||| || |||||| ||||||||||||| || |||||||| |   |||| ||  | || |  | || || ||| ||  || | |||    ||||   |||||  | |   |  |  |||||   | ||  |    || |   ||  |||| ||  |||| |||| |  |||| |||| |||
AAGATCAGATGGTCGTTTCATGGACTGGTCTAAACGTTTGAAGGTTGCCCTGGGTGCTGCCAGAGGTCTAGCTTTCTTACATGATGAAGGACCGTTTCAGgtgagcatgctacttgatttatggtcttatggcatcacataaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataatacc-gagccactgacttaa-cttgtatttatatttccatttgtttttcag

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G380227_T02 (Zea mays), 5'ss of exon 2
-----------------------------------AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttac--tgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacag
                                   |||||| |||||||||||||||||||||||   ||||||||||||||| || |||||||| ||||| || |||||| | ||||||||||| || |||||||| |   |||| ||  | || |  | || || ||| || ||| | |||    ||||   |||||  | |   |  |  ||| |   | ||  |    || ||  ||  |||| ||  |||| |||| |  |||| |||| |||
CTTTATCATGGAAGCTTAGATAAGCTACTCTTTGGAAGATCAGATGGTCGTTTCATGGACTGGTCTAAACGTTTGAAGGTTGCCCTAGGTGCTGCCAGAGgtctagctttcttgcatgatgaaggaccctttcaggtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataatacc-gagctgctgacttaa-ctggtatttatatttccatttgtttttcag

upper sequence: LOC_Os01g60700.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G380227_T01 (Zea mays), 5'ss of exon 2
AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttac--tgcttctaaactttttctttt-tgacattac-caataagtgaatattta---ttttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgtt-attttttttacag
|||||| |||||||||||||||||||||||   ||||||||||||||| || |||||||| ||||| || |||||| | ||||||||||| || |||||||| |   |||| ||  | || |  | || || ||| || ||| | |||    ||||   |||||  | |   |  |  ||| |   | ||  |    || ||  ||  |||| ||  |||| |||| |  |||| |||| |||
AAGATCAGATGGTCGTTTCATGGACTGGTCTAAACGTTTGAAGGTTGCCCTAGGTGCTGCCAGAGGTCTAGCTTTCTTGCATGATGAAGGACCCTTTCAGgtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataatacc-gagctgctgacttaa-ctggtatttatatttccatttgtttttcag

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|29684563|gb|CB680838.1|CB680838
EST:     TTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAG                         GCCATGTACAATGACTT
genomic: TTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttactgctt ... ttttttacagGCCATGTACAATGACTT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATCGGATGGTCGTTTCATGGACTGGTCAGCACGTTTGAAGGTTGCTCTTGGTGCTGCTAGAGGCCTGGCTTTCCTACATGATGAAGGGCCTTTTCAGgttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT