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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggagcatgaactagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaagaattatcaactacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 4
------------------------------------gtaatgga-gcatgaac-tagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaaga--attatcaa-ctacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC
                                    || ||| |    | ||  ||||| ||   |          |   |||  |    ||  || | | || ||||  | |  |  |||| ||| ||  ||| ||  ||| |  |     ||| |||| ||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||||||
gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaatatagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 4
gtaatggagcatgaactagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaagaattatcaactacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC
                                | || | |   || |     |||| ||  |  |  || |    |  |||||     | | |  |||  || ||     |  ||  ||||||||||||||||| ||||||| ||||| ||||| ||||||||||| |     ||   
-------------------------------gtatgttgttgagtcttattcttgagtgcatgttcattattactactattattttgaatgatgattc--actatt----tcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
gtaatggagcatgaactagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaagaattatcaactacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC
                                | || | |   || |     |||| || ||  |  || |  | |  |||||     | | |  ||| |       |  |  ||  ||||||||||||||||| ||||||| ||||| ||||| ||||||||||| |     ||   
-------------------------------gtatgttgttgagtcttattcttgagtgtttgttcattattatgactattattttgaatgatgattcca------tatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 4
gtaatggagcatgaactagatttttttttttttttgctttccggtttatggt--ttgattg--gtttctttttctcttaagaattatcaactacgttttttctaaccatacacatttttcatg----cagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC
           |   |||   |||  | | || ||| ||     ||||||||  |  | ||  |  | | |||    |     |  | || |  |  | |       ||| | |   |  |||    ||||||||||| ||| | ||||| ||| ||||||||||||||||||| || || ||| |
----------gtatgctatcatttgctgtcttgttggttatgaatttatggtggtcaactgtggagtttctttagtctgtttctccttaatttagaatgtctgtgtgatagaaaacctgaatggttgcagGTTATGGACATGCTTGGACCAAGCTTGTGGGATGTTTGGAATAATAACTCTCACAC

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 4
gtaatggagcatgaactagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaagaattatcaactacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC
        | |||  | |  | |||| | | ||||   ||  | |||       |  || | |   |||   ||| | |||   ||  ||| |      |||| | ||     | ||| ||||||||||||||| | ||||| ||  |||||||||||||||||||||| || ||| |
--------gtatgtgccaagtattttatgtgtttt---ttatgattttataacagtgtgatctagcttttctttatggatttagaatgacgatggagaaaacctttcaa----tgcatacagGTTATGGATATGCTTGGACCTAGTTTGTGGGATGTTTGGAATAACAACTCACACAC

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|29688778|gb|CB685053.1|CB685053
EST:     GTGTCCCACGGGTACACTACAAAGGAAAGCAGGGCGGGTTTTACATCATG                         GTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCC
genomic: GTGTCCCACGGGTACACTACAAAGGAAAGCAGGGCGGGTTTTACATCATGgtaatggagc ... tttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCC
EST: gi|29630440|gb|CB635449.1|CB635449
EST:     GTGTCCCACGGGTACACTACAAAGGAAAGCAGGGCGGGTTTTACATCATG                         GTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCC
genomic: GTGTCCCACGGGTACACTACAAAGGAAAGCAGGGCGGGTTTTACATCATGgtaatggagc ... tttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcttaagaattatcaactacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC
                            ttctaac  putative branch site (score: 1)
                                         catttttc  putative PPT
     ttaagaattatcaa  TA-rich tract