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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAACCAGCTGCCATTCAGTATGGCACTGGTTCAATTGCTGGGTTTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcactatatatctcggttaacttactgattattatctctgatcatattgccccaaatatttttaacattgttgcttcaccgctttag

Basic information

species Oryza sativa
transcript LOC_Os05g49200.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G065757_T02 (Zea mays), 5'ss of exon 4
GAAAACCAGCTGCCATTCAGTATGGCACTGGTTCAATTGCTGGGTTTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcac-tatatatctcggttaactt--actgattattatctctgatcatattgccccaaatatttttaacattg-ttgcttcaccgctttag-----
||||||| |||||||| |  ||||| |||||||| |||||||| |||||||| |||||||| |||||| ||||||||||||||||||| ||||||||  |  |  |  | | || ||| | ||  |  |   | | |   |    || ||        ||  |     |  | |||    |  |  |  |     
GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAGgttagtgcacacttgtatctgtttatttgtatgggacagtgttattatgtatgttatggtcgctacatcggtgagggattggagaaggggatcggtgagg
















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|25800141|gb|CA756102.1|CA756102
EST:     TTCAGCGAGGATAGTGTTACAGTNAGGTGATCTGGGTTGTGAAAGATCAG                         GAATTCATTGAAAGCTACCA-GGAGCCAGGTCTTACTTTCATGGTTGCNAA
genomic: TTCAGCGAGGATAGTGTTACAGT-AGGTGATCTGG-TTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAA-GCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAA
EST: gi|58655126|gb|CK043806.1|CK043806
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTAC
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTAC
EST: gi|58672084|gb|CK060770.1|CK060770
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGG
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGG
EST: gi|29639173|gb|CB644182.1|CB644182
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29673512|gb|CB669787.1|CB669787
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29660449|gb|CB656724.1|CB656724
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29643320|gb|CB648327.1|CB648327
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29675128|gb|CB671403.1|CB671403
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29660445|gb|CB656720.1|CB656720
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58658759|gb|CK047439.1|CK047439
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|86908029|gb|CI298797.1|CI298797
EST:     TGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29657722|gb|CB653997.1|CB653997
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29687486|gb|CB683761.1|CB683761
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58670333|gb|CK059019.1|CK059019
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|88385492|gb|CI564152.1|CI564152
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29615519|gb|CB620531.1|CB620531
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29669082|gb|CB665357.1|CB665357
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29660989|gb|CB657264.1|CB657264
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29627821|gb|CB632832.1|CB632832
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58694996|gb|CK083683.1|CK083683
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29677506|gb|CB673781.1|CB673781
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|8251272|gb|AU091468.1|AU091468
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29642551|gb|CB647558.1|CB647558
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58670154|gb|CK058840.1|CK058840
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58666874|gb|CK055560.1|CK055560
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGT
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGT
EST: gi|218478948|gb|FG952780.1|FG952780
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTG-AAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58681561|gb|CK070248.1|CK070248
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29636406|gb|CB641415.1|CB641415
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|163927035|gb|EG710226.1|EG710226
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29644200|gb|CB649207.1|CB649207
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58673500|gb|CK062186.1|CK062186
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTAC
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTAC
EST: gi|58600047|gb|CK010575.1|CK010575
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCCAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29664332|gb|CB660607.1|CB660607
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29681831|gb|CB678106.1|CB678106
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|29639939|gb|CB644948.1|CB644948
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|428757|gb|D24912.1|D24912
EST:     CTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: CTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
EST: gi|58671799|gb|CK060485.1|CK060485
EST:     TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAG                         GAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA
genomic: TTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAA

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), 73 (downstream exon)
Score: 287

GAAAACCAGCTGCCATTCAGTATGGCACTGGTTCAATTGCTGGGTTTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcacta ... accgctttagGAATTCATTGAAGCTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTTGGATTTCAGGAAATATCCGTTGGAGATG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAACCAGCTGCCATTCAGTATGGCACTGGTTCAATTGCTGGGTTTTTCAGCGAGGATAGTGTTACAGTAGGTGATCTGGTTGTGAAAGATCAGgtctgcactatatatctcggttaacttactgattattatctctgatcatattgccccaaatatttttaacattgttgcttcaccgctttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA