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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgctacgctccctgtacctaataaagttctggggcttactccatttgtcgtaaaccgctggttgatgttgcaccgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g71256.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71256.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G028685_T01 (Zea mays), 3'ss of exon 4
gtgtgtgctacgc-tccctgtacctaataaag----ttctggggcttactccatttgtcgtaaaccgctggttga----tgttgcaccgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG
||  ||| | ||  |     |  | || |||     ||||   |||| |||||||| ||| ||      |    |    |||   |  ||||||||| | || |||||||| || |||||| | || || ||||||||||| ||||||||||| || |  ||
gtacgtgttgcggatttgcctttccaaaaaatctttttctattgcttcctccatttctcgcaatttagggaacaagttctgtacaattgttgcagGTCTGGAAGTGTTTGACTCGGAGCTTCTACTGAACGGTATTGTCACTCAGAAGCTAGAGTTCGCCAG
















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|88476623|gb|CI413894.1|CI413894
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88474576|gb|CI411847.1|CI411847
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88519353|gb|CI447007.1|CI447007
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88473139|gb|CI410410.1|CI410410
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88501874|gb|CI429380.1|CI429380
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88478004|gb|CI415275.1|CI415275
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88284730|gb|CI406176.1|CI406176
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88831405|gb|CI083799.1|CI083799
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88515283|gb|CI442937.1|CI442937
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88503548|gb|CI431054.1|CI431054
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88482756|gb|CI420027.1|CI420027
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88281624|gb|CI403020.1|CI403020
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88217255|gb|CI217104.1|CI217104
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
EST: gi|88477716|gb|CI414987.1|CI414987
EST:     AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACG                         GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA
genomic: AATCTCTTGTGAACAAGACTACAAAATATGCGTGCCATTCATTAAGAACGgtgtgtgcta ... accgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgctacgctccctgtacctaataaagttctggggcttactccatttgtcgtaaaccgctggttgatgttgcaccgttgcagGTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC