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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtacagtttgcatacaaaatcttcatgctacggcttgctgcttcatatgccattttatccttatctacttcatttgatgcatccatgttttatttcagGACAAGTACAGGCAGAAAACTCATTTCTCAAAATTTGGAATTCCGTTACCTGACTTTGTGGAA

Basic information

species Oryza sativa
transcript LOC_Os01g10280.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10280.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G133121_T02 (Zea mays), 3'ss of exon 3
----------tagtacagtttgcatacaaaatcttcatgctacggcttgctgcttcatatgccattttatccttatctacttcatttgatgcatccatgttttatttcagGACAAGTACAGGCAGAAAACTCATTTCTCAAAATTTGGAATTCCGTTACCTGACTTTGTGGAA
           | | |   ||    |    || ||  | |  |  || |   |    ||    ||| | ||  |   || ||  ||   || |||  |  |  ||| ||||||||||||||||||||||  |||||||||| ||  |  || || || ||||||||  |||||
gtaagctgatcactgctacttattcatctgattttgttacgccaact-gtaacactttaacaaattgtctcactga-tagtttgtt--gtgtatcggtaatcaattgcagGACAAGTACAGGCAGAAAAAGCATTTCTCAAGATACGAGATCCCATTGCCTGACTTCATGGAA
















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|66917582|gb|CX104430.1|CX104430
EST:     AACAGGGCATCGATTGTGAGCCCAAAGCCTCCACCATCATGATTATTCAA                         GACAAGTACAGGCAGAAAACTCATTTCTCAAAATTTGGAATTCCGTTACCT
genomic: AACAGGGCATCGATTGTGAGCCCAAAGCCTCCACCATCATGATTATTCAAgtaaactttc ... tttatttcagGACAAGTACAGGCAGAAAACTCATTTCTCAAAATTTGGAATTCCGTTACCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgccattttatccttatctacttcatttgatgcatccatgttttatttcagGACAAGTACAGGCAGAAAACTCATTTCTCAAAATTTGGAATTCCGTTACCTGACTTTGTGGAA
                            atttgat  putative branch site (score: 5)
                                            ttttatttc  putative PPT
                                         atgttttattt  TA-rich tract