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

ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattcaacttgttgcataactcgacttcttgttgcgtggctgaatctgtagtatgttcttgtgtcacaatgttagtcatggacttctggttgcat...

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G044237_T03 (Zea mays), 5'ss of exon 15
ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattcaactt----gttgcataactcgacttcttgttg-cgtggctgaatctgtagta-tgttcttgtgtcacaatgttagtcatggacttctggttgcat
||   | || ||||||||||| ||||||||||||||   |||||||||||| ||||||||| |||||||||||||||||||| |||     ||||| || |||| |    | |  |     | ||| | |  |  ||||  | | ||         ||     || ||||||     
ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTGgtaagcattcagcttctttattgca-aattcgagtggaggctaacaatctttaatttattatggtgtttatttatctttgcacctgttcaaaacatctggt-----
















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|58665134|gb|CK053820.1|CK053820
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86600761|gb|CI356518.1|CI356518
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88427802|gb|CI554310.1|CI554310
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|27546388|gb|CA767223.2|CA767223
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAAGGAAGTGGGAAAGGCCTGGGGGCTGTGATTTAAGNTATA
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGA-GGAAGTGG-AAAGGCCTGGGG-CTGTGATTTAAGTTATA
EST: gi|88907071|gb|CI376143.1|CI376143
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86417804|gb|CI032013.1|CI032013
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86483772|gb|CI126405.1|CI126405
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88381110|gb|CI525880.1|CI525880
EST:     GACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|58675407|gb|CK064094.1|CK064094
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86494844|gb|CI137477.1|CI137477
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|218488450|gb|FG961506.1|FG961506
EST:     GTAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGTCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88413541|gb|CI526103.1|CI526103
EST:     CATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: CATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88385172|gb|CI561828.1|CI561828
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88254735|gb|CI353559.1|CI353559
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAG
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAA-GTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAG
EST: gi|88267004|gb|CI378939.1|CI378939
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86600773|gb|CI356530.1|CI356530
EST:     AAAGATGCTGGAGACATCCATGGTACAAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: AAAGATGCTGGAGACATCCATGGTAC-AGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|89162406|gb|CI099098.1|CI099098
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGAGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|87020790|gb|CI269507.1|CI269507
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86499008|gb|CI141641.1|CI141641
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88461401|gb|CI526909.1|CI526909
EST:     TGAACATTGATGTATCANTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: TGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|89168167|gb|CI109371.1|CI109371
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|86433912|gb|CI094255.1|CI094255
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88263131|gb|CI366905.1|CI366905
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88257574|gb|CI360160.1|CI360160
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|29613227|gb|CB618240.1|CB618240
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|87012910|gb|CI297137.1|CI297137
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAG
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAG
EST: gi|86490354|gb|CI132987.1|CI132987
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT
EST: gi|88259524|gb|CI363817.1|CI363817
EST:     GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCACTTG                         GGAGGGGAGGAGGAAGTGGAAAGGCCTGGGACTGTGATTTAAGTTATAAGT
genomic: GAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattc ... tatctgccagGGAGGGGAGGAGGAAGTGGAAAGGCCTGGGGCTGTGATTTAAGTTATAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTGgtaagcattcaacttgttgcataactcgacttcttgttgcgtggctgaatctgtagtatgttcttgtgtcacaatgttagtcatggacttctggttgcat

- - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - TGGAGA