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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatatatcctgtaaattccgtattgtgttattcatgttacacaaagttgtagtttaaccacttaaaatattgtctaatctccatttatttcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACAGAGAAGAGTGTTAGCTTAAGTGTCCTCCAGCAGTACTTCTCTGGCAGCC

Basic information

species Oryza sativa
transcript LOC_Os11g16290.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g16290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 5
-----ctatatatcctgtaaattc-cgtattgtgt-tattcatgttacacaaagttg-tagtttaaccacttaaaatattgtctaatctccatttatttcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACAGAGAAGAGTGTTAGCTTAAGTGTCCTCCAGCAGTACTTCTCTGGCAGCC---------------------------
     |||  |   |   || ||  | || | | |  ||  |  ||  |     | | | || ||||   ||  ||||||  | ||    ||| |  || || || ||  ||  || || | |||     | |    ||| |||    | ||  || ||||||||| ||||||||| ||||||||||| || ||||| ||||| || |                           
gtctgctaattgagcaaaaagttggcatagtttatgcataaactttgtaagttatcggtggtgtaacagtttttaatatttccaaagacacatcttcttgttgtgtagg-aaagaaatggatcaaaaagacaggtccagAAAAATA--GAAGTACATCAGAGAAGAATGTTAGCTTGAGTGTCCTCCAACAATACTTTTCTGGTAGTCTGAAGGATGCCGCAAAAAACATTGGTG
















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|88691534|gb|CI733612.1|CI733612
EST:     AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAG                         TTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
genomic: AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAGgttgtttcat ... tcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
EST: gi|88688917|gb|CI732493.1|CI732493
EST:     AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAG                         TTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
genomic: AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAGgttgtttcat ... tcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
EST: gi|58687769|gb|CK076456.1|CK076456
EST:     AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAG                         TTAATAAAGTGTAGCAATGCATCCGATGGAGAGAAAAGACGCAGCTCAACA
genomic: AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAGgttgtttcat ... tcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
EST: gi|88688760|gb|CI732336.1|CI732336
EST:     AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAG                         TTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
genomic: AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAGgttgtttcat ... tcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA
EST: gi|58610755|gb|CK038467.1|CK038467
EST:     AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAAGAAG                         TTAATAAAGTGTAGCAATGCATCCGATGGAGAGAAAAGACGCAGCTCAACA
genomic: AGATAGAGGGCATTGATGAACAACTATCAGATACAAAAAGTACTAACAAGgttgtttcat ... tcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgtagtttaaccacttaaaatattgtctaatctccatttatttcttttgaagTTAATAAAGTGTAGCAATGCATCCGACGGAGAGAAAAGACGCAGCTCAACAGAGAAGAGTGTTAGCTTAAGTGTCCTCCAGCAGTACTTCTCTGGCAGCC
                           gtctaat  putative branch site (score: 3)
                                 tctccatttatttctt  CT-rich tract
                 ttaaaatattgtctaa  TA-rich tract