Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccttgtgtattctttagatttctaaaagcaatgtaatgacaggaaaaatactaattcatataactttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGCTCCCTGGATTTGTCTTTTGATGATGATTCTGTTGCTGACGAAAAAATAC

Basic information

species Oryza sativa
transcript LOC_Os05g01470.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 6
gttccttgtgtattcttta--gatttctaaaagcaatgtaatgacaggaaaaatactaat----tcatataactttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGCTCCCTGGATTTGTCTTTTGATGATGATTCTGTTGCTGACGAAAAAATAC
||| ||| ||| |||| ||  ||| ||||| || |||    ||||||    |||| || |    | ||  ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||||| |
gttacttttgtgttctctaatgatctctaagagtaataatgtgacagttggaatagtactcttattattgaactttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGATTCCATGAAGTCAGCAGTTCCCTTGATTTATCCTTTGACGATGATTCTGTAGCTGAGGAAAAAATTC

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 6
----gttccttgtgta---ttctttagatttctaaaagca-atgtaatgaca-ggaaaaatactaattcata----------ta-actttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGCTCCCTGGATTTGTCTTTTGATGATGATTCTGTTGCTGACGAAAAAATAC
    | | |||  |||    |  |||  |  ||| ||| | || || |  || |||  ||   | || || |          || |||  ||||| ||    |||||||| ||||| ||| |||| || || ||  ||||||||||||| |||||||||||||| || |||||||||||||| || || || |
gtggggtacttcggtaaagcttgttaattcactacaagaatatttatttccatggaggaaatttgatgcacaatgtcgtttgtatactgacagGTTAAAGTTATATTTGATTTTCTAAAACATGGATTTCAAGAGATCAGCAGCTCCCTAGATTTGTCTTTTGAGGACGATTCTGTTGCTGATGAGAAGATTC

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 6
-----gttccttgtgtattctt--tagatttctaaaagca-atgtaatgacaggaaaaa---------tactaattcatata---actttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGCTCCCTGGATTTGTCTTTTGATGATGATTCTGTTGCTGACGAAAAAATAC
     || | |  |  |  |||  ||  |  ||| ||| | || || || || | |  |          ||||  |||| |    |||  ||||| ||    || ||||| ||||| ||| |||| || || ||  || |||||||||| |||||||||||||| || |||||||||||||| || || || |
gtggggtacttcattaaagcttggtaattcactacaagaatatttattgccatggaggaaatttgatgcactaggtcatttgtatactgacagGTTAAAGCTATTTTTGATTTTCTAAAACATGGATTTCAAGAGATCGGCAGCTCCCTCGATTTGTCTTTTGAGGACGATTCTGTTGCTGATGAGAAGATTC

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 7
------------gttccttgtgtattctttagat---ttctaaaagcaatgtaat-gacaggaaaaatactaat--tcatata-actttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGCTCCCTGGATTTGTCTTTTGATGATGATTCTGTTGCTGACGAAAAAATAC
             || | | | ||  || | ||    || |  ||   |||     |  | | | | |  ||||  |   ||| |||  |||||||| | ||| ||||||||||| ||| |||| ||||||||  ||||||| ||| | ||||| |  ||||| ||||||||||||||||| ||||| || |
gtttgaaattcattttcatatttac-ctgtggacatattttgcaactgatggggcaggaaagtatagtgataataatggaatacactaacagGTGAAAACAATTTTTGAGTTTCTCAAAAATGGCTTCCATGAGATCAGCAGTTCCTTAGATTTATTCTTTGAAGATGATTCTGTTGCTGATGAAAAGATTC

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|58673143|gb|CK061829.1|CK061829
EST:     TTTCACATGCTTTGTCAGTGTATAGCTGTCAACTTCGCCAACCCAACCAG                         GTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGC
genomic: TTTCACATGCTTTGTCAGTGTATAGCTGTCAACTTCGCCAACCCAACCAGgttccttgtg ... taactttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGC
EST: gi|25798544|gb|CA754505.1|CA754505
EST:     TTTCACATGCTTTGTCAGTGTATAGCTGTCAACTTCGCCAACCCAACCAG                         GTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGC
genomic: TTTCACATGCTTTGTCAGTGTATAGCTGTCAACTTCGCCAACCCAACCAGgttccttgtg ... taactttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttctaaaagcaatgtaatgacaggaaaaatactaattcatataactttcagGTGAAGAAAATATTTGAGTTTCTTAAAGATGGGTTCCATGAAGTCAGCAGCTCCCTGGATTTGTCTTTTGATGATGATTCTGTTGCTGACGAAAAAATAC
                                                ctttc  CT-rich tract
                            aaaaatactaattcat  TA-rich tract