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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatttcagtggtccttttgatttaaattttacaattcagagtctaatgccatttaccacacgctgtatggaagtgatatttgatttctgctttt...

Basic information

species Oryza sativa
transcript LOC_Os03g39640.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G153928_T03 (Zea mays), 5'ss of exon 4
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatttcagtggtccttttgatttaaattttacaattcagagtctaatgccatttaccacacgctgta--tggaagtgatatttgatttctgctttt
||| ||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| |  |||||| | |    ||||| || |||| || ||| |  | ||  | |||  ||   ||      |||  | |||       | ||  | || ||  
ATT-TAACATTAGAAGACGTAGTGGAAGAAATAGTTGGTGAAATCTTCGATGAGAATGATTCCAAGgt-gattatttctg-gaattttttgtttaaaatattgcaaatgggtgttcagtgctgttagtcagttttggtagctagaatcagggctagacatatgattac

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA14G01920.1 (Glycine max), 5'ss of exon 11
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatttcagtggtccttttgatttaaattttacaattcagagtctaatgccatttaccacacgctgtatggaagtgatatttgatttctgctttt
||||||||  | ||||||||||| || ||||| ||||| |||||||| ||||| ||||| ||||||||      ||    |    ||||   ||     |||  |||  |   |  |||  |    |    |   | ||| ||| |  |   |  || ||   |||
ATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAGgtaaatgcttgtgcttaatctttactttgtttcttttaaatatatttttaaataactgaaagtgaagcatatattgaattcctccatctttactctgttt

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA02G46780.1 (Glycine max), 5'ss of exon 11
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatttcagtggtccttttgatttaaattttacaattcagagtctaatgccatttaccacacgctgtatggaagtgatatttgatttctgctttt
||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||      ||    |    ||||   ||     |||  |||| |   |  |||  |    |    |   | ||| ||| | ||   |  || ||   |||
ATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAGgtaaatgcttgtgcttaatctttactttgtttcttttaaatttatttttaaataactgaaagtgaagcatatattgaattcatccatctttactctgttt

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 5'ss of exon 11
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttg-gctatttcagtggtccttttgatttaaattttacaattcagagtctaatgccatttaccacacgctgtatggaagtgatatttgatttctgctttt-
|| |||||  | |||||||| || || ||||| || || |||||||||||||||||||||||||| ||   |||   |   |     ||   | ||   ||||   |||    | |       |||   | | |  || ||||     |  |||  |    |   |  
ATAGTAACCCTGGAAGATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAAgtaaagctccctttatatcttttggaactttgtttttggtattttatgacattcataattcctctctca-tgaatggtt-ccacgtttagtggtggaagtgg

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 5'ss of exon 14
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatt---tcagtggtcctttt--gatttaaattttacaattcagagtctaa---tgccatttac-cacacgctgtatgg--aagtgatatttgatttctgctttt---------------------------------------------------------------------
 |||||||  | ||||||||||||||||| || ||||| || || |||||||| |||||||||||||||||  |||   |    |||| | ||  |   | ||    |   ||| || || |    ||| |    | ||   ||||    |  ||| |||  |  |  | | || |                                                                      
GTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAGgttggtcattgtttacaaggtcttgtttgggaatgaacaacatctttctgaatcgatccttgcaaccagctcatgagctgccacgttaagagatcatgcacatttactatgctgaggtgcatacttgtacacctatatcatcaggctttaattggggggctcttggacttgtgaatgcag

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 5'ss of exon 13
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatttcagtgg--tcct--tttga----tttaaat---tttacaattcagagtctaatgccatttaccacacgctgtatggaagtgatatttgatttctgctttt---------------------------------------------------------------------
 |||| ||| | ||||||||||||||||| || ||||| ||||| || ||||| |||||||| |||||||| ||||||  ||   ||||  |||||    |  ||||   |||     |||        | |   ||      |  |   |  ||| ||  ||  |     | | |                                                                      
GTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAGgttggttatttccctgaattcctattttgaaaactagaaatgcctttttgtctcaaccctcgctactggttcatgagctttcagttcaagggactttgcagggtagttatgctaaaacttatatttgtgtatgtacatcaccatccttaaacttctctgctcatggaaatttgtttccag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAGgttggctatttcagtggtccttttgatttaaattttacaattcagagtctaatgccatttaccacacgctgtatggaagtgatatttgatttctgctttt

- - - - - - - - - - - TGGAAG
- - - - - - - - - - -  GGAAGA
- - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - GGAGAA