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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatccaacttgttcttgcgtagtttgcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGTTCCAATGCCATTCAAAGGCTGTGGAAATGGGCTCGGAATGATCAAAATC

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 16
---------------------gtttgatccaacttgttcttgcgtagttt-gcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGTTCCAATGCCATTCAAAGGCTGTGGAAATGGGCTCGGAATGATCAAAATC
                      | || ||       ||||| | | ||||  ||||| || ||||| |||  |      |  ||||| | ||| | ||||||||||| |||||||||||||||||||||||||||| ||||||||||| || || || |||||||||||||| |||||||||  ||| || || |||||||
agctgggcgacgcgggggcctctgtggtcgcgtactttctttcttcgtttcacacttgtcatcatggaat-atgtgagggtttaacatcttttgtgtacagGTTGTCCGACTTCTGTACACAAATTCTGGTGTTGGGTTGCTAGCACTAGGGTCAAACGCCATTCAAAGGCTATGGAAATGGAGTCGAAACGAGCAAAATC

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 18
gtttgatccaacttgttcttgcgtagtttgcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGTTCCAATGCCATTCAAAGGCTGTGGAAATGGGCTCGGAATGATCAAAATC
            || |  |   |||  || |||      ||||| ||| || ||   |  | ||| | ||| | ||||||||||| |||||||||||||||||||||||||||| ||||||||||| || || || |||||||||||||| |||||||||  ||| || || |||||||
------gttggtttttcttgatgtatgtttcacacggtatcatggaat-gtgcaagggtttcacatcttttgtgtacagGTTGTCCGACTTCTGTACACAAATTCTGGTGTTGGGTTGCTAGCACTAGGGTCTAACGCCATTCAAAGGCTATGGAAATGGAGTCGAAACGAACAAAATC
















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|58595855|gb|CK006383.1|CK006383
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58679784|gb|CK068471.1|CK068471
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58661141|gb|CK049821.1|CK049821
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29625565|gb|CB630576.1|CB630576
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58606459|gb|CK034492.1|CK034492
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58601227|gb|CK011755.1|CK011755
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACGAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29626131|gb|CB631142.1|CB631142
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29630393|gb|CB635402.1|CB635402
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29625310|gb|CB630321.1|CB630321
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCT
EST: gi|33675602|gb|CF303841.1|CF303841
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGTTCCAATGCCATTCAAAGGCTGTGGAAATGGGCTCGGAATGATCAAAATC
                                 ggctaac  putative branch site (score: 2)
                                    taacaacatttatata  TA-rich tract