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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgtatatgtgtgacactacttgtatgttttggtgctttttcatgaaagttacagccatggaaactaattttataatgcatgtttgctcattttcagGTCCTAATGGTAGTGGAAAAAGCTCCCTTTTCCGGGTTCTTGGGGGACTGTGGCCACTTATGTCAGGCCACATTGTGAAACCTGGTGTTGGCTCTAATCT

Basic information

species Oryza sativa
transcript LOC_Os01g73530.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G375807_T01 (Zea mays), 3'ss of exon 7
-tgtttgtatatgtgtgacactacttgtatgttttggtgctttt---tcatgaaagttacagccatggaaactaattttataatgcatgtttgctcat-tttcagGTCCTAATGGTAGTGGAAAAAGCTCCCTTTTCCGGGTTCTTGGGGGACTGTGGCCACTTATGTCAGGCCACATTGTGAAACCTGGTGTTGGCTCTAATCT
 | | ||| ||||  | |  ||  || ||| | |  || |||||   | ||| ||||| ||||||||| ||    |||||| |||    ||  ||  | |||||||||| ||||||||||||||||||||||||||||| |||||||| || ||||||||| |  | || || || ||||| |||||||||||||| || |||||
ttttatgtgtatgcctaatgctgatt-tatatctatgttcttttgctttatggaagttgcagccatgggaa----ttttatgatgtgccttaacttctatttcagGTCCCAATGGTAGTGGAAAAAGCTCCCTTTTCCGTGTTCTTGGTGGTCTGTGGCCAATGGTATCTGGTCATATTGTCAAACCTGGTGTTGGTTCCAATCT

upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------------------------------------tgtttgtat-atgtgtgacactacttgtatgttttggtgctttttcatgaaagttacagccatggaaactaattttataatgcatgtttgctcattttc----agGTCCTAATGGTAGTGGAAAAAGCTCCCTTTTCCGGGTTCTTGGGGGACTGTGGCCACTTATGTCAGGCCACATTGTGAAACCTGGTGTTGGCTCTAATCT
                                                                                     |||  | | || | | |  ||| || | |||| |     |  ||| | ||       |  ||||    |  ||| | |    ||   ||||  ||||     |||||| ||||| ||||||||||||||||||||||||||||| || || || |||||| | || || || || ||||||||||||||  |||||||| ||||
gtagctatctgagctcttttcagaattcagtggcctttctttctatttttatttattattcattgggcttgagtcagcattgaaagttgatgttatttattat-ctatttctttgttgtaagagtcattcttaaactgatttgtgatggtttattgtttgacatgttattgatgcttcttttgctgaagGTCCAAATGGCAGTGGAAAAAGCTCCCTTTTCCGGGTTCTAGGTGGTCTTTGGCCATTGATATCTGGACATATTGTGAAACCTGGAATTGGCTCTGATCT

upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 23
tgtttgtatatgtgtgacactacttgtatgttttggtgctttttcatgaaagttacagccatggaaactaattttataatgcatgtttgctcattttcagGTCCTAATGGTAGTGGAAAAAGCTCCCTTTTCCGGGTTCTTGGGGGACTGTGGCCACTTATGTCAGGCCACATTGTGAAACCTGGTGTTGGCTCTAATCT
 ||| |||||  ||| |   || |  |||  |||     ||||| |  | ||  |      |   |    | |||| |     ||| |  |  ||   |||||| ||||| ||||||||||| ||| ||||||| |||||| | ||||| |||||| ||      ||     |    | |||   ||  |      ||| 
-gttcgtatagttgttattttattattatacttta----ttttttagaagagggaattttctttgattagaatttaaatcttttgtgtcatatttaaaagGTCCAAATGGAAGTGGAAAAAGTTCCATTTTCCGAGTTCTTAGAGGACTTTGGCCAATTGCAAGTGGAAGACTCTCTAGACCATCTGAGGATGTGGATCA

upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------tgtttgtat--atgtgtgacactacttgtatgttttggtgctttttcatgaaagttacagcca----------tggaaactaattttataatgcat-gtttgctcattttc------agGTCCTAATGGTAGTGGAAAAAGCTCCCTTTTCCGGGTTCTTGGGGGACTGTGGCCACTTATGTCAGGCCACATTGTGAAACCTGGTGTTGGCTCTAATCT
                                                           ||  | ||  |    |||   || ||  |  || |  | |||| |  | | ||| |  |  |          ||     | ||| | | |    |  || || | | ||       |||||| ||||| ||||||||||||||||||||||||||||| || || || |||||| | || || || || || |||||||||||  |||||||| ||||
gtagctatctgaactctctttttagtggccgatttttatttatttttcagggggcttgagtcagcattgaaagttgatgttattt--actttctatttctttgttgtaagagtcattgttaaactgatttttgttggttgattgtttgacatgttattggcgcttctttggctgaagGTCCAAATGGCAGTGGAAAAAGCTCCCTTTTCCGGGTTCTAGGTGGTCTTTGGCCATTGATATCTGGACATATAGTGAAACCTGGAATTGGCTCTGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaagttacagccatggaaactaattttataatgcatgtttgctcattttcagGTCCTAATGGTAGTGGAAAAAGCTCCCTTTTCCGGGTTCTTGGGGGACTGTGGCCACTTATGTCAGGCCACATTGTGAAACCTGGTGTTGGCTCTAATCT
                    aactaat  putative branch site (score: 2)
                                            ctcattttc  putative PPT
                   aaactaattttataat  TA-rich tract