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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag

Basic information

species Oryza sativa
transcript LOC_Os09g15430.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G116952_T04 (Zea mays), 5'ss of exon 3
TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag--------------------------------------------------------------------------------------------------------------------
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| | ||  |||||| ||||||| |||||||||||||| |||||| | | || || ||     |  ||||| |   ||   | || |||  | | || ||| | ||| | || ||                                                                                                                    
TTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAGgtatctgcattgctctc---tgtttcttttgttgtct-gttgaattcacacgtgaccttgctccctttcgccaggttgtgtttggcattccttgcgcttagttgtgttggatatgccattccttttataatgtgtgcagcaatatgctgctgctttccatgcttgatttctgttttgcgtcttcaagaag

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G116952_T07 (Zea mays), 5'ss of exon 3
TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| | ||  |||||| ||||||| |||||||||||||| |||||| | | || || ||     |  ||||| |   ||   | || |||  | | || ||| | ||| | || ||
TTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAGgtatctgcattgctctc---tgtttcttttgttgtct-gttgaattcacacgtgaccttgctccctttcgccag

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G116952_T03 (Zea mays), 5'ss of exon 3
TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag
                                                              | ||  |||||| ||||||| |||||||||||||| |||||| | | || || ||     |  ||||| |   ||   | || |||  | | || ||| | ||| | || ||
-------------------------------------------------------------TATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAGgtatctgcattgctctc---tgtttcttttgttgtct-gttgaattcacacgtgaccttgctccctttcgccag

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G30020.1 (Glycine max), 5'ss of exon 3
---------TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcatt-cata-gcttttctgaactcaa-------tcaactcatgccttactttgttgcctcttgctag
         |||| || || ||||||||||||||||||||||| ||||| ||||| ||||| || ||          |||  |  | | |||||||| ||| |||| |||||   | |     ||  || |||    | ||| ||  | ||       | || | ||  ||  |||  |   ||||||  ||
AAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACAT---------TCATCTGTTGAAGAAGCTCCTAATTTGTACAGgtagcctttcattcattcttgcatttaatcttcagattttaagatattatgaaattatatct-gcttcat-atctcttggcag

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G07570.1 (Glycine max), 5'ss of exon 3
---------TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcc-tatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag---------------------------------------------------------------------------------------------------------------------------
         |||| || || |||||| |||||||||||||||| ||||| ||||||||||| || ||          |||  | || |  |||| || ||  | || ||||||   || ||   | |  | | |  |    ||   |   | ||    |     |      |   | ||   |                                                                                                                            
AAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACAT---------TCATCTGCTGATCAAGCACCTAACTTATACAGgtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcag

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G07690.1 (Glycine max), 5'ss of exon 2
---------TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttc-----ctatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag---------------------
         |||| || || |||||| |||||||| ||||||| ||||| ||||||||||| || ||          |||  | || |  |||| || ||  |||| ||||||   || ||     || | |    |||| | | |    | || |   |        |  |  |      ||   |                      
AAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTATTGTTGGAAATGTATGGATTTTTGGAGGACAT---------TCATCTGCTGATCAAGCACCTAACTTGTACAGgtatagcctctcaacagctcttacatttagcatgtgtttggtaaaacttttttcaagggaaataatcattatttttcaaaaattctctcacgaagctagc

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 5'ss of exon 3
---------TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcattcatagcttttctgaactcaatcaactcatgccttactttgttgcctcttgctag--------
         | ||||| |||||||| || ||||||||||| |||||||||||||| ||||| || |||    ||   || ||| |||   ||     ||   |  |||| | |  |  |   |||  | |||  || ||  ||| || | |  ||  ||    |||    || |||||||           
AGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCTCCCTCTGATGCTCCCAAATTGTACAG-

upper sequence: LOC_Os09g15430.4 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv11s0016g04450.t01 (Vitis vinifera), 5'ss of exon 3
---------TAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACTTT-GTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctttcctatcattcatagcttttctgaactcaatcaactcatgcct-tactttgttgcctcttgctag
         | || || ||||||||||| |||||||| ||||| ||||| ||||||||||| || |||  | ||||   |  |    ||      | |   |||   |   |  || ||| | |||    | |   |||||      ||   || ||   ||| |   |||      |||||   
AGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCTTTTACCGCAGCTCCAAATTTGTACAGgtattagtcaattcttgcttacatattgaccctttattttcactctgcatgaaaatccaacctgtttcttgggattgcttgcag-

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|29670629|gb|CB666904.1|CB666904
EST:     GGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAG                         GCTATGCTTAGCATTCCTTGCACTTAGTTGTGTTGGGTATGCTATTCCCTT
genomic: GGTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCAATATGTATAGgtattttctt ... ctcttgctagGCTATGCTTAGCATTCCTTGCACTTAGTTGTGTTGGGTATGCTATTCCCTT
EST: gi|218500518|gb|FG959268.1|FG959268
EST:     GTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCATATATGTATAG                         GCTATGCCTTAGCATTCCGTGCACTTAGTTGTGTTGGGTATGCTATTCCCT
genomic: GTGGGCACAGCACTTTGTCAGATTCTCAGGAAGCTCCCA-ATATGTATAGgtattttctt ... ctcttgctagGCTATGC-TTAGCATTCCTTGCACTTAGTTGTGTTGGGTATGCTATTCCCT