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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttagactgtctgacatttacattttatagtgtgctaccttgaatgtctattgaagtttgaattgatccatatttatatgggcgtgggtcttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTGGATTACAAAGGACTGTACAAT

Basic information

species Oryza sativa
transcript LOC_Os01g14810.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 5
--------------gttagactgtctgacatttacattttatagtgtgctaccttgaatgtctattgaagtttgaattgatccatatttatatgggcgtgggtcttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTGGATTACAAAGGACTGTACAAT
                |||||  ||||| |||| |||    |  | |   ||    ||  | |  | ||||||||| |||         |  |||   | | | |||| |||||||||| |||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
ttttcaaatgattatgtagacattctga-atttgcat---gtgatctctcacaccaaacattt-ctcaagtttgaactga---------aactggatattgctattctcttcagATGGTTGACAAGTTAGATCAGGGATTGGTGCCAGCTGAACTTGGGCCACTGGATTACAAAGGACTGTACAAT
















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|29627736|gb|CB632747.1|CB632747
EST:     AGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAG                         ATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTG
genomic: AGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAGgtcaattacc ... ttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTG
EST: gi|66923280|gb|CX110128.1|CX110128
EST:     AGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAG                         ATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTG
genomic: AGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAGgtcaattacc ... ttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTG
EST: gi|29673384|gb|CB669659.1|CB669659
EST:     AGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAG                         ATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTG
genomic: AGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAGgtcaattacc ... ttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctattgaagtttgaattgatccatatttatatgggcgtgggtcttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTGGATTACAAAGGACTGTACAAT
               aattgat  putative branch site (score: 4)
                                           tcttctgttc  putative PPT
                    atccatatttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactgtctgacatttacattttatagtgtgctaccttgaatgtctattgaagtttgaattgatccatatttatatgggcgtgggtcttctgttcagATGGTCGACAAGTTGGATCAGGGGTTGGTGCCAGCTGAACTTGGGCCACTGGATTACAAAGGACTGTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA