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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcactgattctcaacttggcagaagggtgctattgaacaattataaacacatcatcttagactatcagacaagcaaagttttctctttttctctctccttccttttcattttagggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA

Basic information

species Oryza sativa
transcript LOC_Os01g01070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G078711_T01 (Zea mays), 3'ss of exon 5
gtaatcactgattctcaacttggcagaagggtgctattgaacaattataaacacatcatcttagactatcagacaa-gcaaagttttctctttttctctctcctt--ccttttcattttagggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA
                                                             |  |  || | |||  | ||| | | ||  |  | |  || ||   || ||| || || |  ||| ||||| | |||   | |            ||||| ||  ||||| |||||| ||||||||||||||| |||||||||||||||||||||| ||||||||||| ||| |||| || || |||||  |||| || |||||||| | |||||
-------------------------------------------------------------tgaatgattatacactgtaaactgtgctaatggtattcctactgtgccatttgatatttgaccaa-tgtca-attccgttaga------------gctaattcaatgatt-acagGGGTGGAAACTTTCTGATATGATGTTTGTGACGAAGCGTGGATTATCTGATGCTTGCAATGTTGTGGGGAAACAAGTGGATCAGGTTTCAGAAAGTGTTA

upper sequence: LOC_Os01g01070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147587_T01 (Zea mays), 3'ss of exon 5
gtaatcactgattctcaacttggcagaagggtgctattgaacaattataaacacatcatcttagactatcagacaa-gcaaagttttctctttttctctctcctt--ccttttcattttagggcaactgtcataatccacaaaatggggcaatcaagctaactcggtgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGATGCCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTA
                                                             |  |   | | |||| | ||| | | ||  |  |  | || ||   || ||| || || || ||  |   ||  ||||  | |            ||||||||| ||||| |||||| ||||||||||||||| |||||||||||||||||||||| ||||| ||||| ||| |||| || || |||||  |||| || |||||||| | |||||
-------------------------------------------------------------tgaatggttatacaatgtaaactgtgctaatgctagccctactgtaccatttgatgtttggccagtttcaat--tccatcaga------------gctaactcgatgatt-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|58593533|gb|CF991841.1|CF991841
EST:     CTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGG-----                         G-TTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: CTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGGTAAAAgtaatcactg ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
EST: gi|88315903|gb|CI618779.1|CI618779
EST:     CTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGG-----                         G-TTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: CTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGGTAAAAgtaatcactg ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
EST: gi|58687220|gb|CK075907.1|CK075907
EST:     CTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAA-G-----                         GGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: CTGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGTGGAAGGTAAAAgtaatcactg ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
EST: gi|33658119|gb|CF280733.1|CF280733
EST:     TGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGGGTGGAAGGTAAAA                         GGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT
genomic: TGTTGTTGCTGGGGCTATCGGCTATTTATACATAAGG-TGGAAGGTAAAAgtaatcactg ... tgatttacagGGTTGGAAACTTTCTGATTTGATGTTTGTGACGAAGCGTGGCTTATCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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