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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatacctacatgaaagataggtgtaaagtgcaacatacatttgtatagcattgtctgtgatagttgaatagttggttgacctagtacatgagaacataaaaacaagatgatgccttatagaattttacttcttgtagAATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGGTCTATTGCCACATCAGATGCAAGGATCGCTCTCAAAGTGTGTCTTGTCA

Basic information

species Oryza sativa
transcript LOC_Os01g42850.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42850.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 12
gtaagtatacctacatgaaagataggtgtaaagtgcaacatacatttgtatagcattgtctgtgatagttgaatagttggttgacctagtacatgagaacataaaaacaagatgatgccttatagaattttacttcttgtagAATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGGTCTATTGCCACATCAGATGCAAGGATCGCTCTCAAAGTGTGTCTTGTCA
                                                    | |   |   | | || | | |  |  ||  | ||  |   |  |||       || |  || |||| ||   |   |  | | ||  || || |  || ||||| |||| |||||||||||| || || ||||| ||||||||||||||||||||| | | |||||| ||| | |||||||  || |  
----------------------------------------------------gtaagataccttaaagattattgctgagtccaacttatgtttatgaagtc---caccatgtggtgccataagtatcataccctttttcagGATACGGGCCCCAGGCGATACTGCTGGTACAGAAACAGAACATCAACTTGGTCTATTGCCACATCAGCTACGAGGATCACTCCCCAAGTGTGATTTATTT
















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|33677842|gb|CF306081.1|CF306081
EST:     TCTGGCAAAGCAGTGGAGCTCTTTGCTAGGATGTTACATCATCCAGATGA                         AATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGG
genomic: TCTGGCAAAGCAGTGGAGCTCTTTGCTAGGATGTTACATCATCCAGATGAgtaagtatac ... cttcttgtagAATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGG
EST: gi|29640244|gb|CB645253.1|CB645253
EST:     TCTGGCAAAGCAGTGGAGCTCTTTGCTAGGATGTTACATCATCCAGATGA                         AATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGG
genomic: TCTGGCAAAGCAGTGGAGCTCTTTGCTAGGATGTTACATCATCCAGATGAgtaagtatac ... cttcttgtagAATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGG
EST: gi|29674599|gb|CB670874.1|CB670874
EST:     TCTGGCAAAGCAGTGGAGCTCTTTGCTAGGATGTTACATCATCCAGATGA                         AATTCATGCTC
genomic: TCTGGCAAAGCAGTGGAGCTCTTTGCTAGGATGTTACATCATCCAGATGAgtaagtatac ... cttcttgtagAATTCATGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtacatgagaacataaaaacaagatgatgccttatagaattttacttcttgtagAATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGGTCTATTGCCACATCAGATGCAAGGATCGCTCTCAAAGTGTGTCTTGTCA
                                        ttttacttctt  CT-rich tract
                                ttatagaattttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatacctacatgaaagataggtgtaaagtgcaacatacatttgtatagcattgtctgtgatagttgaatagttggttgacctagtacatgagaacataaaaacaagatgatgccttatagaattttacttcttgtagAATTCATGCTCCAGGAGATATTGCTGGTACAGACACTGAGCATCAGCTTGGTCTATTGCCACATCAGATGCAAGGATCGCTCTCAAAGTGTGTCTTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG