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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccttttatgttcatactcccatgtatactcacactgcattaattttctgtctctgttttgatgataatatcttttaacttattgccatttgcctgcagGCAGTTCTAGCTTTATATGCTGCTAAACGAACTTCTGGTATTGTTGTCAACATTGGATTTAATGCCACATCTATTGTTCCTA

Basic information

species Oryza sativa
transcript LOC_Os04g57210.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57210.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G043862_T01 (Zea mays), 3'ss of exon 6
atccttttatgttcatactcccatgtatactcacactgcattaattttctgtctctgttttgatgataatatcttttaacttattgccatttgcctgc-agGCAGTTCTAGCTTTATATGCTGCTAAACGAACTTCTGGTATTGTTGTCAACATTGGATTTAATGCCACATCTATTGTTCCTA
|| ||||    ||  || |  |||  ||   ||||    ||| |    || ||| ||  |  |   | ||     | | || | || ||||||  | | ||||||||||| |||| |||||| ||||||| || ||||||||||||||  |||||||||| ||| | || ||| ||||||| |
attctttgtaatttgta-tgtcattcatttgcacaacatatttacaaactatctttgagtatacttttatgagcatgagctcactggcatttggtttctagGCAGTTCTATCTTTGTATGCTTCTAAACGGACCTCTGGTATTGTTGTGCACATTGGATTCAATACGACTTCTGTTGTTCCCA
















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|66925992|gb|CX112840.1|CX112840
EST:     ACTCGGTTCTGTTCGATATGAATGTTCCTGCTGTTTGTTCTGTTGATCAG                         GCAGTTCTAGCTTTATATGCTGCTAAACGAACTTCTGGTATTGTTGTCAAC
genomic: ACTCGGTTCTGTTCGATATGAATGTTCCTGCTGTTTGTTCTGTTGATCAGgtgtgcattc ... ttgcctgcagGCAGTTCTAGCTTTATATGCTGCTAAACGAACTTCTGGTATTGTTGTCAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtctctgttttgatgataatatcttttaacttattgccatttgcctgcagGCAGTTCTAGCTTTATATGCTGCTAAACGAACTTCTGGTATTGTTGTCAACATTGGATTTAATGCCACATCTATTGTTCCTA
                            ttttaac  putative branch site (score: 2)
                                            tttgcct  putative PPT
            ttttgatgataatatc  TA-rich tract