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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtaatcactgattctcaacttggcagaagggtgctattgaacaattataaacacatcatcttagactatcagacaagcaaagttttctctttttctctctccttccttttcattttagggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA

Basic information

species Oryza sativa
transcript LOC_Os01g01070.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G078711_T01 (Zea mays), 3'ss of exon 5
gtaaaagtaatcactgattctcaacttggcagaagggtgctattgaacaattataaacacatcatcttagactatcagacaa-gcaaagttttctctttttctctctcctt--ccttttcattttagggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA
                                                                   |  |  || | |||  | ||| | | ||  |  | |  || ||   || ||| || || |  ||| ||||  ||| |           |  |  |||||| ||  ||||| |||||| ||||||||||||||| |||||||||||||||||||||| ||||||||||| ||| |||| || || |||||  |||| || |||||||| | |||||
-------------------------------------------------------------------tgaatgattatacactgtaaactgtgctaatggtattcctactgtgccatttgatatttgaccaa-tgtc--aattc-----------cgttagagctaattcaatgatt-acagGGGTGGAAACTTTCTGATATGATGTTTGTGACGAAGCGTGGATTATCTGATGCTTGCAATGTTGTGGGGAAACAAGTGGATCAGGTTTCAGAAAGTGTTA

upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147587_T01 (Zea mays), 3'ss of exon 5
gtaaaagtaatcactgattctcaacttggcagaagggtgctattgaacaattataaacacatcatcttagactatcagacaa-gcaaagttttctctttttctctctcctt--ccttttcattttagggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA
                                                                   |  |   | | |||| | ||| | | ||  |  |  | || ||   || ||| || || || ||   ||   ||| |           ||    |||||||||| ||||| |||||| ||||||||||||||| |||||||||||||||||||||| ||||| ||||| ||| |||| || || |||||  |||| || |||||||| | |||||
-------------------------------------------------------------------tgaatggttatacaatgtaaactgtgctaatgctagccctactgtaccatttgatgtttggcca---gtttcaattc-----------catcagagctaactcgatgatt-acagGGGTGGAAACTTTCTGATATGATGTTTGTGACGAAGCGTGGGTTATCAGATGCTTGCAATGTAGTGGGGAAACAAGTGGATCAGGTTTCAGAAAGTGTTA
















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|33658119|gb|CF280733.1|CF280733
EST:     TGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGGTGGAAG
genomic: TGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGG-TGGAAG
EST: gi|88315903|gb|CI618779.1|CI618779
EST:     TAACAGCTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAG                         GGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: TAACAGCTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGgtaaaagtaa ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
EST: gi|58593533|gb|CF991841.1|CF991841
EST:     TAACAGCTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAG                         GGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: TAACAGCTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGgtaaaagtaa ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
EST: gi|58687220|gb|CK075907.1|CK075907
EST:     TAACAGCTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAG                         GGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: TAACAGCTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGgtaaaagtaa ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA
                                  agctaac  putative branch site (score: 2)
        tcataat  TA-rich tract