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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCATTCCGTCCCCATGGCTGTTGACGATCTAAACCACCACCTCATCGCCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatttcttctttaattaactcactctgtgatcgatcagatcacctgcattaattcgttcatctatctatctatctatcacatacgcgtagtaagtaagaagtatgatttgaaataatagatggcgcatgcag

Basic information

species Oryza sativa
transcript LOC_Os10g42780.1
intron # 1
splice site 5'
intron type U2

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|88574922|gb|CI666691.1|CI666691
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88310130|gb|CI657554.1|CI657554
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88339829|gb|CI649086.1|CI649086
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88851858|gb|CI679416.1|CI679416
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88583755|gb|CI701259.1|CI701259
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88585677|gb|CI703333.1|CI703333
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88307119|gb|CI640554.1|CI640554
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|29660093|gb|CB656368.1|CB656368
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCATGGCGCATGC               
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCG---CA-----C---Cgtgagcaatt ...
EST: gi|29660093|gb|CB656368.1|CB656368
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCATGGCGCATGC               
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCG---CA-----C---Cgtgagcaatt ...
EST: gi|29660093|gb|CB656368.1|CB656368
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCATGGCGCATGC               
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCG---CA-----C---Cgtgagcaatt ...
EST: gi|88412239|gb|CI573515.1|CI573515
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88345362|gb|CI656020.1|CI656020
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88586573|gb|CI704279.1|CI704279
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88325554|gb|CI675361.1|CI675361
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88423952|gb|CI689449.1|CI689449
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88387053|gb|CI577839.1|CI577839
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|700761|gb|D47052.1|D47052
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGNCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAN-TGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88328785|gb|CI646855.1|CI646855
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|29676078|gb|CB672353.1|CB672353
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTAGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTT-GTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGC
EST: gi|88385895|gb|CI568563.1|CI568563
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|58590558|gb|CF988866.1|CF988866
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88584351|gb|CI701899.1|CI701899
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88345286|gb|CI655746.1|CI655746
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88369932|gb|CI680612.1|CI680612
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
EST: gi|88410459|gb|CI686392.1|CI686392
EST:     CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACC                         CTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC
genomic: CCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatt ... gcgcatgcagCTTGTGCGGAATATGGCGCAGCTGGTGGTGTCGCTGGGCATATTGGTCGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCATTCCGTCCCCATGGCTGTTGACGATCTAAACCACCACCTCATCGCCGTCGGAGTCGGAGAAGAAGCCGCCACCGCCCATTGTGGGCTGCGCACCgtgagcaatttcttctttaattaactcactctgtgatcgatcagatcacctgcattaattcgttcatctatctatctatctatcacatacgcgtagtaagtaagaagtatgatttgaaataatagatggcgcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC