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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttgtgccaactatggtagatatattaatgtcgaaaactcatccactcggtggagttttttttaaagaacttttttaagtttactttccagtgtaatagaagctaactgtggtgttagcaccttttttttttttgcagaaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCT

Basic information

species Oryza sativa
transcript LOC_Os03g01750.5
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G052546_T04 (Zea mays), 3'ss of exon 9
gtatgcttttgtgccaactatggtagatatattaatgtcgaaaactcatccactcggtggagttttttttaaagaacttttttaagtttactttccagtgtaatagaagctaactgtggt-gttagcaccttttttttttttgcagaaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCT
                                                                                                 | |  ||    | | |    |    |   |   ||   | |||||     |   | ||            || |   ||||||  |||| | ||      ||||| |||||||||||||||  |  |||||||| ||||||||| ||||||||  |||||||||
------------------------------------------------------------------------------------------------ggggctatgatggttgaacaagcccatctacctgttacatgtttttattagatataatcccgtgcataagtctctaactgatttctatttatcct-----ttcagAGAATTCCTTTGACATATGATGAGGAGAAAGGAGCTTGGTTTCTTGAGAAAGAGTTGCCT
















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|29656092|gb|CB652367.1|CB652367
EST:     TTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: TTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|88311093|gb|CI658006.1|CI658006
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|58688312|gb|CK076999.1|CK076999
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|2428616|gb|C73079.1|C73079
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|29626840|gb|CB631851.1|CB631851
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|58696174|gb|CK084861.1|CK084861
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|58694687|gb|CK083374.1|CK083374
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
EST: gi|29656147|gb|CB652422.1|CB652422
EST:     CTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGGCATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: CTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCT
                                            tgcttac  putative branch site (score: 2)
                                         ttctgctt  CT-rich tract
     attcttaattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttttgtgccaactatggtagatatattaatgtcgaaaactcatccactcggtggagttttttttaaagaacttttttaagtttactttccagtgtaatagaagctaactgtggtgttagcaccttttttttttttgcagaaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG