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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagctgaattataaggattgctacctttgagggtcttaaagttgtaaacattgtattgtatattcttgatatgggactatgtatgctgatgatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTGATCGCTCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCT

Basic information

species Oryza sativa
transcript LOC_Os11g23790.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g23790.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA03G22370.1 (Glycine max), 3'ss of exon 1
cagctgaattataaggattgctacctttgagggtcttaaagttgtaaacattgtattgtatattcttga---tatgggactatgtatgctgatgatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTGATCGCTCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCT
 |  | | ||||     ||| | ||||||   | | |  |||       | ||| |  | |  || ||    | |   | ||||| |    ||  |  |  || ||||||||||| | ||||| |     |  ||   | |||| |||||||||   || |||||||| ||||| || |||||||||||||||||||| |  |
-aaat-atttattgttcttggt-cctttgcatgacatgtagtgaatcctaatgtgtgatgtggtcatgcgcctgtattattatgtgtataaatttttatccagTTGGAAGACATGAATATGGACGAGGAATCAGAGAAAGTGGCAGTGGAGTTGGCTGCACAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAATCCGATT
















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|88724678|gb|CI747937.1|CI747937
EST:     TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTG                         ATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTG
genomic: TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggttt ... gatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTG
EST: gi|88355934|gb|CI653344.1|CI653344
EST:     TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTG                         ATGGAAGACATGGA
genomic: TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggttt ... gatgctgtagATGGAAGACATGGA
EST: gi|66914314|gb|CX101162.1|CX101162
EST:     TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTG                         ATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
genomic: TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggttt ... gatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
EST: gi|29615880|gb|CB620892.1|CB620892
EST:     TCCGCGGCGGCGAGCAGGTCGCCTCCGTACTCCAGGAGATGCTCAAGCTG                         ATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
genomic: TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggttt ... gatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
EST: gi|29673555|gb|CB669830.1|CB669830
EST:     TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTG                         ATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
genomic: TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggttt ... gatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
EST: gi|33658439|gb|CF281052.1|CF281052
EST:     TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTG                         ATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG
genomic: TCCGCGGCGGCGAGCAGGTCGCCTCCGTGCTCCAGGAGATGCTCAAGCTGgtacgggttt ... gatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacattgtattgtatattcttgatatgggactatgtatgctgatgatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTGATCGCTCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCT
                                      tgctgat  putative branch site (score: 3)
     ttgtattgtatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagctgaattataaggattgctacctttgagggtcttaaagttgtaaacattgtattgtatattcttgatatgggactatgtatgctgatgatgctgtagATGGAAGACATGGAGATGGATGGCTCGTTTGAATCATTGGCTGTGGAGTTGATCGCTCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA