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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgaaatactagctggcaaaggctgcctttcttcctctgtaactagaactttgtgttcctttgatatatcagtgattttaacttttgattcctcgctcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G18370.1 (Glycine max), 3'ss of exon 11
--gtttgtgaaatactagctggcaaag--gctgcctttcttcctctgtaactagaactttgtgttc----ctttgatat-----atcagtgattttaacttttgattcctcgct---cccatttagGGT-TGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG
    ||   ||  ||    |  ||||      |    |||  |  |||||  | | |||| ||||     ||||| | |     ||    |    ||| |  ||||   | | |   |  ||||  |   |||| | ||   | |||  | ||    | | |  | ||  |||||||| | ||||| |||||||||||||||||||||||||| ||||||
gtaattcctaaccacctattcacaaaataaaagaaaatctcgccatgtaataaaagctttatgttggctactttgttgttgttaattgacgtagataattgatgataaattgttaaccatatttcagTCGTGGATTACCCTGAGGGCAAGAGAAACAGCTGCCTTGGGGAGAGAATTGCTTGGTGGCAATGGAATTTTGGCTGATTTTCTAGTGGCAAAG

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G43240.1 (Glycine max), 3'ss of exon 11
--gtttgtgaaatactagctggcaaag--gctgcctttcttcctctgtaactagaactttgtgttc----ctttgatat-atcagtgattt--------taacttttgatt---cctcgctcccatttagGGT-TGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG
    ||   ||  ||    |  ||||      |    | |  |   ||||  | | |||| ||||      |||| | |  | | | | ||        |||||  ||||      ||  ||   |||  |   |||| | ||   | |||  | ||    | | |  | ||  |||||||| | ||||| |||||||||||||||||||||||||| ||||||
gtaattcctaaccacctattcacaaaataaaagaaaatatcaccaagtaataaaagctttatgttggctattttgttgttgttaataaattgaggtagataactggtgataaaatgtcaatcatgtttcagTCGTGGATTACCCTGAGGGCAAGAGAAACAGCTGCCTTGGGAAGAGAATTGCTTGGTGGCAATGGAATTTTGGCTGATTTTCTAGTGGCAAAG

upper sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 11
gtttgtgaaatactagctggcaaaggctgcctttcttcctctgtaa-ctagaactttgtgttcctttgatatatcagtgattttaacttttgattcctcgctcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG
                                   |   | || || || ||  |      ||| ||  |   | | |  |  |||| | |  |||  |  |     | |||  ||||   ||   | |||  | |||    || |||| || || || ||  | ||||| |||||||| ||||||||||||||||||||||||
----------------------------------gtgaatatgaaatctggagatgcagactccatt--ttactgactagtcataacatat--ttctccaatgtatatcagGCATGGATCACCTTGAAGGCAAGGGAGACTCTTGCTCTTGGGCGTGAGTTACTAGGTGGCAATGGAATCTTGGCTGATTTTCTAGTTGCAAAG

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|29658082|gb|CB654357.1|CB654357
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|86504925|gb|CI147558.1|CI147558
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGCCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGNTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|33683999|gb|CF312238.1|CF312238
EST:     GCTTTATGAGTCAGGGAAAATGACACCAGGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATT
genomic: GCTTTATGAGTCAGGGAAAATGACACCA-GGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTT-CCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATT
EST: gi|44666104|gb|CR279538.1|CR279538
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGATGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|4715706|gb|AU056822.1|AU056822
EST:     GCTTTATGAGTCAGGGAAAATGACCACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: GCTTTATGAGTCAGGGAAAATGA-CACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|7839222|gb|AU090633.1|AU090633
EST:     CTTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: C-TTTATGAGTCAGGGAAAATGACACCAGGGCATGC-TAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|29668419|gb|CB664694.1|CB664694
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|29660317|gb|CB656592.1|CB656592
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAG                         GGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG
genomic: AGCTTTATGAGTCAGGGAAAATGACACCAGGGCATGCTAGTTTAGGGAAGgtttgtgaaa ... tcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttcctttgatatatcagtgattttaacttttgattcctcgctcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG
                                     ttcctcgctcccattt  CT-rich tract
                       attttaacttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgaaatactagctggcaaaggctgcctttcttcctctgtaactagaactttgtgttcctttgatatatcagtgattttaacttttgattcctcgctcccatttagGGTTGGACTTCCAGAATGGCTCGTGAGGTGGTTTCTCTCGGTCGAGAATTGTTGGGTGGAAATGGAATTTTGGCTGATTTTCTAGTTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG