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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgcaatactatgcatggatagagaccatccatagaatatatagtagtagctctttcagttcagttcaccgtaattgatagttcttcacttcagctcttatgtttcacgcaagtttagtgtctatgattaattagctgaccataatgatctgattctgatgatgcagGTTTTGGCTACTGATGAGTTCTGGCCGGCACAAGGAGGGAAAGCACCAGAGCTCTCTCAAGTCAAGGACGCCTTGGACGCCATCCTATCTTCTCAGCATC

Basic information

species Oryza sativa
transcript LOC_Os01g02110.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G066057_T01 (Zea mays), 3'ss of exon 3
------------------------gtatattgcaatactatgcatggatagagaccatccatagaata-tatagtagtagctctttcagttcagttcaccgtaattgatagttcttcacttcagctcttatgtttcac-gcaagtttagtgtctatgattaattagctgaccataatgatctgattctg-atg-atgcagGTTTTGGCTACTGATGAGTTCTGGCCGGCACAAGGAGGGAAAGCACCAGAGCTCTCTCAAGTCAAGGACGCCTTGGACGCCATCCTATCTTCTCAGCATC
                         |||||  |  |  | |   |      |    || ||| | ||  ||   | |||     | ||  || |||    || || |   | |   |    ||| |   |     |   | |||| || | ||   | || ||   || |   |||||   | || ||| ||| |||||||| |||||| | |||||||||||||| ||||||||||| || |||||||| ||||| ||||| ||||||||||||||||||||||| || ||    || |
gtacgtggcgaaggctgtctgatcatatatatctgtcatttagttttggctaccttatgcatgggatggtaacatggtactatctccatctccgtt----gttatcgtccgctaaacgtgacagataaaaaagaacggaggaagtatattatcccagcttcat---ctaat--taatggattcatgctgcatgcatgcagGTGTTGGCTGCCGATGAGTTCTGGCCTGCACAAGGAGGCAAGGCACCAGACCTCTCCCAAGTGAAGGACGCCTTGGACGCCATCCTGTCATCGTCCCAGC

upper sequence: LOC_Os01g02110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G37800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatattgcaatactatgcatggatagagaccatccatagaatatatagtagtagctctttcagttcagttcaccgtaattgatagttcttca-cttcagctc---ttatgtttcacgcaagtttagtgtctatgattaattagctgaccataatgatctgattctgatgatgcagGTTTTGGCTACTGATGAGTTCTGGCCGGCACAAGGAGGGAAAGCACCAGAGCTCTCTCAAGTCAAGGACGCCTTGGACGCCATCCTATCTTCTCAGCATC
                                                                   | || | | |||   | | | | ||| ||  |  ||    |||||   |   ||||   || | |    |  |||     |    ||  | ||   |||  |  |  ||||  | ||  | |||||||| ||||||||||||||||||||||| || ||  | |||||||| || || ||  | ||||| ||||| || ||    || |
-----------------------------------------------------------------gtaattaatcttaacaaacattccgtcaactatatatcatactatgtcatatataagtagggtctttcaagtatattgatataaacaaaaaaactatgtctttt--tatagGTACTTGCAGCCGATGAGTTTTGGCCGGCACAAGGAGGGAAAGCTCCGGACATTTCTCAAGTTAAAGAAGCTATTGACGCAATCCTCTCATCATCACAAC
















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|86500245|gb|CI142878.1|CI142878
EST:     TGCTAGAAAAGGCGATCAACTACGTCAAATTCCTCCAGCTGCAAGTGAAG                         GTTTTGGCTACGGATGAGTTCTGGCCGGCACCAAGGAGGGAAAGCACCAGA
genomic: TGCTAGAAAAGGCGATCAACTACGTCAAATTCCTCCAGCTGCAAGTGAAGgtatattgca ... gatgatgcagGTTTTGGCTACTGATGAGTTCTGGCCGGCA-CAAGGAGGGAAAGCACCAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttagtgtctatgattaattagctgaccataatgatctgattctgatgatgcagGTTTTGGCTACTGATGAGTTCTGGCCGGCACAAGGAGGGAAAGCACCAGAGCTCTCTCAAGTCAAGGACGCCTTGGACGCCATCCTATCTTCTCAGCATC
                                         ttctgat  putative branch site (score: 3)
        tctatgattaatta  TA-rich tract