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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattacctaacttgtagttaaaaggttcacattgcattaaattaatagaattttgttttattacctgtattgttgacccaacctcatttcattcagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG

Basic information

species Oryza sativa
transcript LOC_Os04g11880.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 11
gtaagtattacctaac-ttgtagttaaaaggttcacattgcattaaattaatagaattttgttttattacctgtattgttgacccaacctcatttcattcagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG
|||||||   |||||   |||| ||  | |   |||||   || ||| || || | |||| ||      |   |  | |  |   || | |||||  |||||||| ||||||||||||||||||| |||||||||||  ||||||||||||||||||||||||| |||
gtaagtacatcctaaagctgtatttgtagg---cacat---atcaaaata-tacatttttattgc----caaattctttctaattaaacccatttggttcagCTCCTGAAGCCAGAAGTATTCGAGTTTATTGAGAAATACAACTTGCATGATGCCATTCATGATAAG

upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA12G08840.1 (Glycine max), 3'ss of exon 11
-----------------------------gtaagtattacctaacttgtagttaaaaggttcacat-tgcattaaattaatagaattttgttttattacctgtattgttgacccaacctcatttcatt---------------cagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG
                             | | | |  | | ||| |  | ||||| |    ||   |||  |  | ||  |   | |||| |  ||   |  | || | |  ||  ||| |||  ||               ||||| ||||||||||||||||| || |||||||| || || ||| | || ||||| |||| ||  |||
gtaagtgttcgaagaattttttcttaaatgcaggcagcaac-aacat-caattaaatgtcatacgcatgctgtgtactag-aatctgttgtctatttgttttaactgctaattcactctccttttttttttggttgaaattttcagCTTTTGAAGCCAGAAGTATTTGATTTTATTGATAAACATAACCTACACGATGCTATTCGTGGAAAG
















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|58675059|gb|CK063746.1|CK063746
EST:     TGTATGTCATCAACAGTCAATATGACAAGGCCCTTTCTCTGTATGCTGAA                         CTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGAT
genomic: TGTATGTCATCAACAGTCAATATGACAAGGCCCTTTCTCTGTATGCTGAAgtaagtatta ... tttcattcagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGAT
EST: gi|66914272|gb|CX101120.1|CX101120
EST:     TGTATGTCATCAACAGTCAATATGACAAGGCCCTTTCTCTGTATGCTGAA                         CTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGAT
genomic: TGTATGTCATCAACAGTCAATATGACAAGGCCCTTTCTCTGTATGCTGAAgtaagtatta ... tttcattcagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatagaattttgttttattacctgtattgttgacccaacctcatttcattcagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG
                             tgttgac  putative branch site (score: 3)
                                        cctcatttc  putative PPT
     agaattttgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattacctaacttgtagttaaaaggttcacattgcattaaattaatagaattttgttttattacctgtattgttgacccaacctcatttcattcagCTCTTGAAGCCAGAAGTATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC