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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTGGGGAAGTGGCGCGGGGAAGGCGAGGGGAGCTTCCCCACCATCTCCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacctcctcgcctgtatctgtatatctctttcgctcgccaaagcttttaccttttctcgaccatgccgcacgcag

Basic information

species Oryza sativa
transcript LOC_Os01g48760.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48760.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G092152_T02 (Zea mays), 5'ss of exon 1
CCTGCTGGGGAAGTGGCGCGGGGAAGGCGAGGGGAGCTTCCCCACCATCTCCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacctcctcgcc------tgtatctgt---------atatctctttcgctcgccaaagctttta--ccttttctcgaccatgccgcacgcag-----------------
||| ||||||||||||||||||||||||||||| |||||||||||||| ||| ||||||| ||||||||||||||||||||||| || || ||||||||||     | ||  |||  |      ||| ||| |         || |  | ||||   ||||||   ||    | ||||||    | | | |  ||  |                 
CCTACTGGGGAAGTGGCGCGGGGAAGGCGAGGGCAGCTTCCCCACCATATCCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggccctctctacctgcgatgtttctctcgcgagaaaatcttcccttcggctgccaaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcag

upper sequence: LOC_Os01g48760.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv19s0085g01130.t01 (Vitis vinifera), 5'ss of exon 1
---CCTGCTGGGGAAGTGGCGCGGGGAAGGCGAGGGGAGCTTCCCCACCATCTCCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacctcctcgc-ctgtatctgtatatctctttcgct--cgccaaagcttttaccttttctcgaccatgccgcacgcag----------------
   ||||||||| |  ||| | ||  ||||||||||  | ||||||||||||  | |||||  |||||||||||||||||||||||| ||     |   |||||||  |    | |||   ||  ||   |     ||||| | |   |   |||    |  ||||| ||   | |       |                   
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCA---TTCGGGCAAGgtactcctttttctctttctaaatacttcctcttcttttgatgatgatgaagacgatgacttttttctttccttttttctgtttttctttgttgaaaaag
















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|86898820|gb|CI296101.1|CI296101
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88825494|gb|CI776059.1|CI776059
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88317589|gb|CI672171.1|CI672171
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTNGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88761445|gb|CI771001.1|CI771001
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCC
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGC-AGAGGACGTGGAAGGCGGCGTCAGGCGAGCC
EST: gi|88665244|gb|CI710078.1|CI710078
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88587859|gb|CI705639.1|CI705639
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88734582|gb|CI758090.1|CI758090
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88580222|gb|CI692224.1|CI692224
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|86850381|gb|CI307610.1|CI307610
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCA-CCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88593295|gb|CI709458.1|CI709458
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|56157672|gb|C25211.2|C25211
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88210949|gb|CI212589.1|CI212589
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|87012916|gb|CI297143.1|CI297143
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|25799413|gb|CA755374.1|CA755374
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88761851|gb|CI771407.1|CI771407
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG

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: 28 (upstream exon), 48 (downstream exon)
Score: 1

CCTGCTGGGGAAGTGGCGCGGGGAAGGCGAGGGGAGCTTCCCCACCATCTCCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTGGGGAAGTGGCGCGGGGAAGGCGAGGGGAGCTTCCCCACCATCTCCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacctcctcgcctgtatctgtatatctctttcgctcgccaaagcttttaccttttctcgaccatgccgcacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC