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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGGGAACGCTATGGACGCCGCCGAACGGGTCGGCCGCCAGGCCGAGCGCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttcaaacccttgaatccccagggccacggtcctctcgcctgacctcttgtgatcacagctcgacttgatgcgcatgcttgttttttttttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g53250.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53250.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G069865_T02 (Zea mays), 5'ss of exon 2
GACTGGGAACGCTATGGACGCCGCCGAACGGGTCGGCCGCCAGGCCGAGCGCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttcaaacccttgaatccccagggccacggtcctctcgcctgacctcttgtgatcacagctcgacttgatgcgcatgcttgttttttttttttcag
 ||||||||||| ||||||||||| || || || |||||| |||| || || ||||||||||||||||||||||| ||| |||||||||||||||| ||||| |||| |||| ||| ||  || |||   |||   ||   |   ||    ||||    |   |   |  ||  |||                        
AACTGGGAACGCCATGGACGCCGCAGAGCGTGTGGGCCGCGAGGCAGAACGTGGCGGCTGCCCGGCCGTCGACGTGCTCTCCATGGACAGCTTCGATCCCgtgagctccaaaacctagagccctcagccacacaacccgtgcatgtgcgaacttgacgcctttgtgtg--ttcgtgcag----------------------
















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|88335855|gb|CI645456.1|CI645456
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         ACTTGCCTTCCGAGCGACAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88722798|gb|CI746308.1|CI746308
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88741622|gb|CI765130.1|CI765130
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88734893|gb|CI758401.1|CI758401
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88357086|gb|CI615973.1|CI615973
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88736011|gb|CI759519.1|CI759519
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88761113|gb|CI770669.1|CI770669
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88315483|gb|CI613752.1|CI613752
EST:     GCGGGGGCTGCCCGGCCGTAGAGGTCCTCCCCATGGACAGCTTCGACACC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTC-ACCAAGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88302768|gb|CI668614.1|CI668614
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88740589|gb|CI764097.1|CI764097
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88733930|gb|CI755440.1|CI755440
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88763614|gb|CI773061.1|CI773061
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88739468|gb|CI762976.1|CI762976
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88733643|gb|CI756820.1|CI756820
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88422716|gb|CI573878.1|CI573878
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|88340678|gb|CI647556.1|CI647556
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
EST: gi|87015558|gb|CI303164.1|CI303164
EST:     GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCC                         AGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG
genomic: GCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 45 (downstream exon)
Score: 26

GACTGGGAACGCTATGGACGCCGCCGAACGGGTCGGCCGCCAGGCCGAGCGCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttca ... tttttttcagAGTTGCCTTCCGAGCGAGAGGTTCGTGGTCTTCGTCGTGTCCACCACGGGGCAGGGTGATCCCCCGGATTCCATGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGGGAACGCTATGGACGCCGCCGAACGGGTCGGCCGCCAGGCCGAGCGCGGCGGCTGCCCGGCCGTCGACGTCCTCCCCATGGACAGCTTCGACCCCgtaagcttcaaacccttgaatccccagggccacggtcctctcgcctgacctcttgtgatcacagctcgacttgatgcgcatgcttgttttttttttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA