Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGATTAGAAAGAAGAGGGTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgatgatataaacattttcatggttttgctgggctctagataataaaaatgaagagtttaactctgttttcagacaataattcgtagcctactttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os07g27790.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 14
AATGGATTAGAAAGAAGAGGGTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgatgatataaacattttcatggttttgctgggctctagataataaaaatgaagagtttaactctgttttcagacaataattcgtagcctactttgttgcag
|||||||| ||||||||||| ||||||||||| |||||| | ||||||||||| | |||| | ||  ||||| |  | | | |||||| ||||||      |||         | ||  | ||     |  |     |  |  |   | |  |   | |  |  |||||  |   | |||                             
AATGGATTGGAAAGAAGAGGATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgt-agtagtgctacattc-agcatcctcggccat--------gtttacgctttgctgcgaatcactcgttccgtttctgaagatcctaattaacttaacctttgctacag-----------------------------

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 14
AATGGATTAGAAAGAAGAGGGTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgatgatataaacattttcatggttttgctgggctctagataataaaaatgaagagtttaactctgttttcagacaataattcgtagcctactttgttgcag
|||||| | |||||||||||||||||||||||||||||| | |||||||| || | |||  | ||  ||||  ||   |        ||  |||||   ||| ||  |     |||     || | | | |  |  |   ||  |  |    | |                                                      
AATGGACTGGAAAGAAGAGGGTACAAGGAGGTTGGTTTCCTTAGAGAGGTCGACGAAGTAGTGAGAACAGgcaaatgctattcagcaccctcatcttcattcgtttgttggactatctgt-ttctgaagatcctaattaccttcaacttgctacag-----------------------------------------------------
















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|86250888|gb|CI007751.1|CI007751
EST:     GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|29682926|gb|CB679201.1|CB679201
EST:     GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|29682925|gb|CB679200.1|CB679200
EST:     GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAT                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|29679437|gb|CB675712.1|CB675712
EST:     GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|218493685|gb|FG958530.1|FG958530
EST:     GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|88974786|gb|CI023082.1|CI023082
EST:     TAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: TAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC

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: 71 (upstream exon), 21 (downstream exon)
Score: 8

AATGGATTAGAAAGAAGAGGGTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAACGCAGCGTCGATCCTGTCTTCCAGGAGTTGTTATACTGATGCTGAGAAAC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGATTAGAAAGAAGAGGGTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgatgatataaacattttcatggttttgctgggctctagataataaaaatgaagagtttaactctgttttcagacaataattcgtagcctactttgttgcag

- - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - -  GAGAGG