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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctattttctgctgttaactcttgttatgacatattaagatgtgttatttaaaccttaatgtcagctgcatattctaaattgccgctcatttttgcagTTTGCTGGGGGATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAGGAATCTTGTGCATGTCAGAAACAGCACCCAGTAGGAAGTTAAAAAAATGT

Basic information

species Oryza sativa
transcript LOC_Os08g03560.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g03560.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G019225_T01 (Zea mays), 3'ss of exon 8
------------gtgctattttctgctgttaactcttgttatgacatattaa---gatgtgttatttaaaccttaatgtcagctgcatattctaaattgccgctcattttt-gcagTTTGCTGGGGGATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAGGAATCTTGTGCATGTCAGAAACAGCACCCAGTAGG-AAGTTAAAAAAATGT
             || ||        |  |  | ||| | | |  |    ||     ||| ||  ||||  ||  |||    || ||   | |||||  | |||||||||| |||||||||||| || |||||||| ||||||||||||||||| || ||||||||||| || || || |||||||||||||||||||||  | |       |  | 
gtaacaaatttgttggtaaacaaaaattatttcccttatcacgggacgggaatctactgtctttgttaagtctgcatgct--cttcagcgtttaaatc-cagctcattttttgcagTTTGCTGGAGGTTTCGATCCGGAGACCATGGATGCATTCGAGGAGCTGAGGAACCTCGTTCACGTCAGAAACAGCACCCAGTAGCTAGGACGCGGCACCG-
















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|33808425|gb|CF330101.1|CF330101
EST:     TGGAGTATATGCTACTTCAGGCTGTGAGATTTGCCTTCAGAATGCATCAG                         TTTGCTGGGGGATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAGG
genomic: TGGAGTATATGCTACTTCAGGCTGTGAGATTTGCCTTCAGAATGCATCAGgtaacacatt ... atttttgcagTTTGCTGGGGGATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAGG
EST: gi|33811209|gb|CF331494.1|CF331494
EST:     TGGAGTATATGCTACTTCAGGCTGTGAGATTTGCCTTCAGAATGCATCAG                         TTTGCTGGGGGGATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAG
genomic: TGGAGTATATGCTACTTCAGGCTGTGAGATTTGCCTTCAGAATGCATCAGgtaacacatt ... atttttgcagTTTGCTGGGGG-ATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttaaaccttaatgtcagctgcatattctaaattgccgctcatttttgcagTTTGCTGGGGGATTCGATCCAGAGACCATGGATGCATTTGAAGAGCTGAGGAATCTTGTGCATGTCAGAAACAGCACCCAGTAGGAAGTTAAAAAAATGT
                             ttctaaa  putative branch site (score: 2)
                                          ctcattttt  putative PPT
                          atattctaaatt  TA-rich tract