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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattttgaaagcttgaatatatgtgctctcgattctcatagtttgtgtataccagcacatgtaactaatagtaaataaagttttaatcctactggcatttttcttctttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAGCCTACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTG

Basic information

species Oryza sativa
transcript LOC_Os03g62640.5
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 5
gtattattttgaaagcttgaatatatgtgctctcgattctcatagtttgtgt-ataccagcacatgtaacta--atagtaaa--taaagttttaatcctactggcatttttctt-ctttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAGCCTACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTG---
|||||| ||  |    |||||    | |  |     || |  |  ||||| |  | ||||||||  | | ||  || |||    |   ||||| ||          |||||  |  |||  |||||||||||||  |||||||||| |||||||||||||||||||||||| |||||||| |||   |||||||| ||||| |||| ||| |||| ||||| ||||   
gtattaattcaattttttgaaagagtatttttattcttatattgatttgtattgttccagcacaaattattataattgtagtgctttggttttgatgtggtaattgttttttctattttcctgcagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAGCCTGCTC---CACCTCAAGTGGCAGCAGTTCCACCACCAGCTCCACCTGATG

upper sequence: LOC_Os03g62640.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 5
gtattattttgaaagcttgaata-tatgtgctctcgattctcata---gtttgtgtataccagcacatgtaact--aatagta--aataaagttttaatcctactggcatttttctt-ctttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAGCCTACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTG
|||||| |||||    ||||  | |||||  | ||  |||| |||    | |   | | ||||||||  | | |  ||| |||  | |  |||||| ||          |||||| |  |||| | |||||||||||  |||||||||| |||||||||||||||||||||||| |||||||| ||| | | |||||| ||||  |||  ||| |||| ||||| || |
gtattaatttgattctttgagaagtatgttttttcatttcttatattgatcttattgttccagcacaaattattcaaattgtagtactttagttttgatttggtaattgtttttcctattttgctccagGCTACCCTCTTGCTTGATGCTTTTAACAAGGACAGAGCTTCATTAACTCAGCCTGCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCG
















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|29681220|gb|CB677495.1|CB677495
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|88689613|gb|CI733189.1|CI733189
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCT
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCT
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|29621718|gb|CB626729.1|CB626729
EST:     AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: AGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
EST: gi|38480710|gb|CF964799.1|CF964799
EST:     TGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG                         GCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG
genomic: TGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAGgtattatttt ... tttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactaatagtaaataaagttttaatcctactggcatttttcttctttgttgcagGCTACCCTTCTGCTTGATGCCTTTAACAAGGACAGAGCTTCATTACCTCAGCCTACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTG
                                  catttttcttctttgt  CT-rich tract
     aatagtaaataaagtt  TA-rich tract