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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatggcattgttacatgttcagataaactgttgaggggtctcgcattgtatatttgtatctagcatggaagttttgatgtgttgatcttgatgcagGTATGCACACCTGTAGATAAAGGGGCACTCTACTATGAGTTTCAGTACAACACAAGATCGGTGAAACCGACAATTCTTCATTTCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g38880.6
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G113726_T01 (Zea mays), 3'ss of exon 2
gcatggcattgttacatgtt-cagataaactgttgaggggtctcgcattgtatatttgtatctagcatggaagt-tttgatgtgttgatcttgatgcagGTATGCACACCTGTAGATAAAGGGGCACTCTACTATGAGTTTCAGTACAACACAAGATCGGTGAAACCGACAATTCTTCATTTCCAG
||||| ||| | |||  ||| ||||| |  | |         |||  |||   || | | |    |  | ||   | | |||||  |||  || |||||| |||||  |||| ||| |||||   ||||||||| ||||||||| ||| ||| || |||||||||||||| || | ||||||||||
gcatgccatagctacgcgtttcagattagttatactacctggtcgagttgagcatctatttaggccgagtaaacatctcatgtggcgatgctggtgcagGAATGCATGCCTGCAGAGAAAGGCCAACTCTACTACGAGTTTCAGCACAGCACGAGGTCGGTGAAACCGACCATCCGTCATTTCCAG
















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|29640492|gb|CB645501.1|CB645501
EST:     AGTACGCGAACTTTGAGAATGTACCCAACTCCGGGAAAAATTCAGAGAAG                         GTATGCACACCTGTAGATAAAGGGGCACTCTACTATGAGTTTCAGTACAAC
genomic: AGTACGCGAACTTTGAGAATGTACCCAACTCCGGGAAAAATTCAGAGAAGgcatggcatt ... cttgatgcagGTATGCACACCTGTAGATAAAGGGGCACTCTACTATGAGTTTCAGTACAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcattgtatatttgtatctagcatggaagttttgatgtgttgatcttgatgcagGTATGCACACCTGTAGATAAAGGGGCACTCTACTATGAGTTTCAGTACAACACAAGATCGGTGAAACCGACAATTCTTCATTTCCAG
                                            tcttgat  putative branch site (score: 4)
       tatatttgtatcta  TA-rich tract