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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG

Basic information

species Oryza sativa
transcript LOC_Os01g09120.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G176506_T04 (Zea mays), 3'ss of exon 2
gtgagttatttgcataatctgt---ttgtattgttgt-----tgttttgacgtatatctcgtgttcaaaataa-atatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG
|||||||||||||||| | |||   || | |||||||     ||| | | | ||| | | ||||| |||| |   ||| | || ||||| |   ||| |||| |  |  |     | |||||||| |||| |||||||||||| |||  |||||| ||||||| || || ||||||||||||||||||  |||| ||||||
gtgagttatttgcatattttgtccattattttgttgtctacttgtctcgtcttat-ttttgtgttgaaaacattgtatgtccaattcatgcgtgcttcattattaaactga----tcattttgaactgat-cacagGACTGACTCCCGCTTGCCTAACATGCCAATTATTTATGCTAGTGATGCTTTTACATCATTAACAG

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G176506_T07 (Zea mays), 3'ss of exon 2
-------------------------gtgagttatttgcataatctgt---ttgtattgttgt-----tgttttgacgtatatctcgtgttcaaaataa-atatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG
                         |||||||||||||||| | |||   || | |||||||     ||| | | | ||| | | ||||| |||| |   ||| | || ||||| |   ||| |||| |  |  |     | |||||||| |||| |||||||||||| |||  |||||| ||||||| || || ||||||||||||||||||  |||| ||||||
gtagaatcaaacagagctttgtattgtgagttatttgcatattttgtccattattttgttgtctacttgtctcgtcttat-ttttgtgttgaaaacattgtatgtccaattcatgcgtgcttcattattaaactga----tcattttgaactgat-cacagGACTGACTCCCGCTTGCCTAACATGCCAATTATTTATGCTAGTGATGCTTTTACATCATTAACAG
















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|29660689|gb|CB656964.1|CB656964
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29660992|gb|CB657267.1|CB657267
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29657673|gb|CB653948.1|CB653948
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29680769|gb|CB677044.1|CB677044
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29662742|gb|CB659017.1|CB659017
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|31818552|gb|CD645551.1|CD645551
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29640574|gb|CB645583.1|CB645583
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29655805|gb|CB652080.1|CB652080
EST:     AGTTGTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GGCTGACCCCCATTTGCCTGACATGCCGATCATGTATGGTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|14571448|gb|BI118816.1|BI118816
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|38474285|gb|CF958417.1|CF958417
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|88228766|gb|CI228246.1|CI228246
EST:     CAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: CAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29660961|gb|CB657236.1|CB657236
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG
                tattaat  putative branch site (score: 2)
                                ttttattttgaaatga  TA-rich tract