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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactcactgttctccttttactagcttgaacttactacataatctgtttgtgttttcctccaacctgtatactgttctcgagttgttcatgtttccatttgatttcaaaacagAAAGGAACTACCGTAGAGAAACTCACTGAGGAAACCTTGAGGGACAAGGATCATCTTAGGAACCTTCTTGCTGTGTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g43400.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 4
gtacactcactgttctccttttactagcttgaacttactacataatctgtttgtgttttcctccaacctgtatact-gttctcgagttgttcatgtttccatttgatttcaaaacagAAAGGAACTACCGTAGAGAAACTCACTGAGGAAACCTTGAGGGACAAGGATCATCTTAGGAACCTTCTTGCTGTGTGTGAAG
                                          | |  |   |      |   |||||  ||||| |  |  |  |  |  | ||| | ||| |  ||||  ||||||| ||||||||  || ||||||||||||||||||||  |||| |||  | | ||||| |   | || ||| |  | || ||||
-----------------------------------------gttagttcccttctcaatgtaccaactagtatatttatatttcaaatactgatggt-ccact--attt--aaacagAGAGGAACTATTGTTGAGAAACTCACTGAGGAAACTCTGAGAGACTGGAACCATCTAATAGAGCTCCTTTCCCTATGCGAAG
















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|88367346|gb|CI566312.1|CI566312
EST:     ACCTCCTGAGCCACGACACCACACCCCTCAGACTTCTTGATGATCCGGAG                         AAAGGAACTACCGTAGAGAAACTCACTGAGGAAACCTTGAGGGACAAGGAT
genomic: ACCTCCTGAGCCACGACACCACACCCCTCAGACTTCTTGATGATCCGGAGgtacactcac ... ttcaaaacagAAAGGAACTACCGTAGAGAAACTCACTGAGGAAACCTTGAGGGACAAGGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaacctgtatactgttctcgagttgttcatgtttccatttgatttcaaaacagAAAGGAACTACCGTAGAGAAACTCACTGAGGAAACCTTGAGGGACAAGGATCATCTTAGGAACCTTCTTGCTGTGTGTGAAG
                                      atttgat  putative branch site (score: 5)
                                      atttgatttcaaaa  TA-rich tract