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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaattacttctgtctacaaccattaggataagttgcctttgacactgatttccttttcttttgcttgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 6
-----gtgaaattacttctg---tctacaaccattaggataagttgcctttgacactgatttccttttcttttgcttgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG
      |  | || | ||||   | |  |  |||  |  ||| |       | |  |    |   ||| |||| ||| |     |||  || ||||||||  ||||||||||||||||||||||| | |  ||||| ||||| ||||| |||
gtgaatttgagttccatctggactttggagtcatctgattaaatgtttccaggcctttggcttgatttatttttcttttctggcagAATCCTCCAAGAAACTTATGGGAGCTTATTCCTAATGCTTCATCTGAAGCAATCGATTTGATCCAG

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA03G21610.1 (Glycine max), 3'ss of exon 10
------------gtgaaattacttc---tgtctacaaccattaggataagttgcctttgacactg-attt--ccttttcttttgcttgttcaaa--------agATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG
            || | |  ||||    ||| ||| |   |||        | |  |   || |  ||||   || ||||||          |         || | || ||    || || |   |  ||||||| ||||||| |||||||||||| ||||||||    
gtaagtgttcgcgtaacaggactttggttgtgtactattcttaattcttaatactgtcatcattttatttaatctattctttaatccccctgatgctggtgcagGTTCCGCCTGTGAAGCTTTCTAATATTATTCCGAATGCTAGTTTGGAAGCTATAGACTTGATCACA
















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|34996388|gb|CF569133.1|CF569133
EST:     GGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAG                         ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
genomic: GGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAGgtgaaattac ... tgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     GGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAG                         ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
genomic: GGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAGgtgaaattac ... tgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     GAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAG                         ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
genomic: GAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAGgtgaaattac ... tgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     GGCCAGNNNGAATGAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAG                         ATCCCACCANNNNNTCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT
genomic: GGCCAGAGGGAATGAACCTGCCTCGTTCAAGCAGCTTTAATTTTTTCCAGgtgaaattac ... tgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaggataagttgcctttgacactgatttccttttcttttgcttgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG
                      cactgat  putative branch site (score: 3)
                            tttccttttcttttgc  CT-rich tract
                                 ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaattacttctgtctacaaccattaggataagttgcctttgacactgatttccttttcttttgcttgttcaaaagATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG