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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagttactgtttctttatgtgttaatatcaatatgaacatgctaatatcatcatgagacaccttttaacaccatgtattagatttgcctctattgtaatgacacaaagaaagatatttgtttgtgcagttatactgaactgtatctcatttctaactatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCATTGCGTGAACTCTTAGGCCATACTCCAACCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g67560.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G059108_T01 (Zea mays), 3'ss of exon 2
gtatgcagttactgtttctttatgtgttaatatcaatatgaacatgctaatatcatcatgagacaccttttaacaccatgtattagatttgcctctattgtaatgacacaaagaaagatatttgtttgtgcagttatactgaactgtatctcatttctaactatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCATTGCGTGAACTCTTAGGCCATACTCCAACCCAG
||||| | | ||    ||| |  |||  |     ||| |      | ||   |    ||          |||  ||| |||  ||| | |   | |||| | || |||           |||||| | ||   ||||  ||||||  || |  |||    | || || ||||  |||| |||||||| || ||||||||||||||||||||||||||||||||||||||| |||| ||||| ||||||||||| |||||||||
gtatgtaataac----tctatgcgtggcatctgtaatgttggttcggtagcctttctata------tcgttacaaccttgtgatagctctctatgtattatgataaca-----------atttgtgt-tgtgcttatgttgaacttaattttgttttctccaatttttagGTACTGAACCAAATAGTTTGTGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACCCAG

upper sequence: LOC_Os01g67560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G091435_T03 (Zea mays), 3'ss of exon 2
gtatgcagttactgtttctttatgtgttaatatcaatatgaacatgctaatatcatcatgagacaccttttaacaccatgtattagatttgcctctattgtaatgacacaaagaaagatatttgtttgtgcagttatactgaactgtatctcatttctaactatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCATTGCGTGAACTCTTAGGCCATACTCCAACCCAG
    | |  || |  ||||||  |||  |     | | |        ||   |     |          |||  ||| |||  ||| | |   | |||| |  | |||           |||||| || |   ||||  ||||||  || |  |||    | ||  | |||| |||||||||||||| || ||||||||||||||||| ||||||||||| ||||||||| |||| ||||| ||||||||||| ||||| |||
----gtacgtaataattctttgcgtgccatctgtactgttggttcaatagcctttctgta------tcgttacaaccttgtgatagctctctatgtattatggtaaca-----------atttgtgtg-gtgcttatgttgaacttaatttagttttctccgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG
















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|58600636|gb|CK011164.1|CK011164
EST:     TTATGTACGATGCTTCTGGTATCAGATTACATGCTGGAAAGCAAGCAGAG                         GTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAA
genomic: TTATGTACGATGCTTCTGGTATCAGATTACATGCTGGAAAGCAAGCAGAGgtatgcagtt ... ctatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAA
EST: gi|88508844|gb|CI436350.1|CI436350
EST:     TTATGTACGATGCTTCTGGTATCAGATTACATGCTGGAAAGCAAGCAGAG                         GTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAA
genomic: TTATGTACGATGCTTCTGGTATCAGATTACATGCTGGAAAGCAAGCAGAGgtatgcagtt ... ctatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAA
EST: gi|88252935|gb|CI350360.1|CI350360
EST:     GCTTCTGGTATCAGATTACATGCTGGAAAGCAAGCAGAG                         GTGTTGAATCAAATAGTCTGCGAACTTCCTTCTG-ACATCCCTTGTCTGAA
genomic: GCTTCTGGTATCAGATTACATGCTGGAAAGCAAGCAGAGgtatgcagtt ... ctatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatatttgtttgtgcagttatactgaactgtatctcatttctaactatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCATTGCGTGAACTCTTAGGCCATACTCCAACCCAG
                                       ttctaac  putative branch site (score: 1)
                                     atttctaactatatt  TA-rich tract