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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttcctgaagatatcgcgttactaggctctgtgtattcgtatttggcttactgtttttcagctttgatgggtcgttgtgggttggggaattggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAGGGGGTCCCTGACGGCGCCGCCGTCCGTCCTACTGTGTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g68010.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 1
gtgagatttcctgaagatatcgcgttactaggctctgtgtattcgtatttggcttactgtttttcagctttgatgggtcgttgtgggttggggaattggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAGGGGGTCCCTGACGGCGCCGCCGTCCGTCCTACTGTGTGGAAG
|| ||   |||||  | |  || ||| || || |              |||| ||  ||  ||  | ||   | ||||| ||| |||| |  | |       ||||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||||| ||||  || | ||||||  | ||||| ||||||
gtaaggcctcctgctgtttgcgtgttgcttggtt--------------ttggtttgttggcttctaactc--aggggtcattgagggt-gatgtacccttctagCTGTCCAAGAAGGTGATAGATCTCGATGAACTGAGGATGCTGGCGGCTCAGGGAGTCCCAGACGCGGCGGGCGTCCGAGCAACTGTATGGAAG
















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|88336570|gb|CI656841.1|CI656841
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|88339196|gb|CI633767.1|CI633767
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|38565749|gb|CK085202.1|CK085202
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|88370350|gb|CI587740.1|CI587740
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|88341320|gb|CI640077.1|CI640077
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|9866162|gb|AU101912.1|AU101912
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|88364426|gb|CI644504.1|CI644504
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
EST: gi|58652950|gb|CK041630.1|CK041630
EST:     CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCG                         CTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG
genomic: CCCCTCCGCCGGAGTTCGAGATCTCGCGGCAGTCCCGTCTCCTCGCGGCGgtgagatttc ... attggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcttactgtttttcagctttgatgggtcgttgtgggttggggaattggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAGGGGGTCCCTGACGGCGCCGCCGTCCGTCCTACTGTGTGGAAG
        tgttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatttcctgaagatatcgcgttactaggctctgtgtattcgtatttggcttactgtttttcagctttgatgggtcgttgtgggttggggaattggcgcagCTGTCCAAGAAGGTGATAGATCTCGATGAGCTGAGGATGCTGGCTGCTCAGGGGGTCCCTGACGGCGCCGCCGTCCGTCCTACTGTGTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG