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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttttttgttagtgcggatatccatgtctaccacttcatcagtcaggctaattgataatgtgacttactctattatttactattcccccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAGAGAGTTGGCACATACGATACTCAG

Basic information

species Oryza sativa
transcript LOC_Os04g52710.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094255_T02 (Zea mays), 3'ss of exon 4
-aattttttttgttagt-----gcggatatccatgtctaccacttcatcagtcaggcta-attgataatgtgacttactctattatttactattcccccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAGAGAGTTGGCACATACGATACTCAG-------------------------
 |  ||| ||||  | |     |   || |   | |   | | || ||  | ||    | |||| | || |       || ||  ||||  | | |||  |||| ||||||| |||||||| |||||||| || || ||||||  |||||| ||| | |||||||||||||| ||||| |||                         
tatatttgtttgccatttttcggttcatgttagtttaatctattttattggacacatcacattggtcatattg-----tcaatgtttta--acttccctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGGTAAATTGTGAAATTTGCAAACCTT

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 4
-aattttttttgttagt-----gcggatatccatgtctaccacttcatcagtcaggcta-attgataatgtgacttactctattatttactattcccccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAGAGAGTTGGCACATACGATACTCAG
 |  ||| ||||  | |     |   || |   | |   | | || ||  | ||    | |||| | || |       || ||  ||||  | | |||  |||| ||||||| |||||||| |||||||| || || ||||||  |||||| ||| | |||||||||||||| ||||| |||
tatatttgtttgccatttttcggttcatgttagtttaatctattttattggacacatcacattggtcatattg-----tcaatgtttta--acttccctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG
















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|29658246|gb|CB654521.1|CB654521
EST:     TTGGGCATTTTACAGCACCACTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAG
genomic: TTGGGCATTTTACAGCACCACTTGATGAGGCAGCGGTTGAGGTTATACTGgtacatgcta ... ccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAG
EST: gi|29676398|gb|CB672673.1|CB672673
EST:     TTGGGCATTTTACAGCACCACTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAG
genomic: TTGGGCATTTTACAGCACCACTTGATGAGGCAGCGGTTGAGGTTATACTGgtacatgcta ... ccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggctaattgataatgtgacttactctattatttactattcccccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAGAGAGTTGGCACATACGATACTCAG
                   gacttac  putative branch site (score: 2)
                                 tttactattccccc  putative PPT
                          tctattatttactatt  TA-rich tract