Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcattctttcatcatctctgcatcccactggaaactgatgacgattgacgagtacaaattttatagagcttatgcaattaaccttctcgctctttttctgcttggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCACTGGTGAAGGCGGCCATGGATGTTGTGGTGGCCGTAGGGCTTCTTCAGC

Basic information

species Oryza sativa
transcript LOC_Os03g02590.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02590.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 5
gtgtgcattctttcatcat---ctctgcatcccactggaaactgatgacgattgacgagtacaaattttatagagcttatgcaattaaccttctcgctctttttctgcttgg---tttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCACTGGTGAAGGCGGCCATGGATGTTGTGGTGGCCGTAGGGCTTCTTCAGC
|||   |  | |  |  |    || |   | |  |     |||| |   | |    |  |  |   | |||  |||| |     |  ||||  | |    |||    | |||   ||   |||| || |||||| ||  ||| ||||  ||||| ||||||||||| || || ||||| |||||||||||||| || || |||||||| |||||||||||||
gtgcatacacatatactacacactttcgtttctgccactgactgtttgaggtgagggcatggagtgtatatgcagct-aaattttccacctgtttgagtgtttatcacatggccattctcagAACGAGCAGTACCAGGACAAAATGAGGCAGTCAGATGAACGGCTCCTGGCCCTGGTCAAGGCGGCCATGGACGTGGTCGTGGCCGTCGGGCTTCTTCAGC

upper sequence: LOC_Os03g02590.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029824_T04 (Zea mays), 3'ss of exon 1
gtgtgcattctttcatcatctctgcatcccactggaaactgatgacgattgacgagtacaaattttata-gagcttatgcaattaaccttctcgctctttttctgcttgg---tttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCACTGGTGAAGGCGGCCATGGATGTTGTGGTGGCCGTAGGGCTTCTTCAGC
                                                 ||| | | |   | | |||| |    ||     |  ||||  | |    |||    | |||   ||   |||| || |||||| ||  ||| ||||  ||||| ||||||||||| || || ||||| |||||||||||||| || || |||||||| |||||||||||||
------------------------------------------------gtga-gggcatggagtgtatatgcagctaaattttccacctgtttgagtgtttatcacatggccattctcagAACGAGCAGTACCAGGACAAAATGAGGCAGTCAGATGAACGGCTCCTGGCCCTGGTCAAGGCGGCCATGGACGTGGTCGTGGCCGTCGGGCTTCTTCAGC
















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|86261335|gb|CI014402.1|CI014402
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|89187844|gb|CI009828.1|CI009828
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88836930|gb|CI008366.1|CI008366
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|218504458|gb|FG953020.1|FG953020
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88984635|gb|CI009411.1|CI009411
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|33662420|gb|CF293387.1|CF293387
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|218490956|gb|FG953067.1|FG953067
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|33664837|gb|CF295804.1|CF295804
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|89195811|gb|CI007230.1|CI007230
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|86415722|gb|CI029733.1|CI029733
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|15854786|gb|BI807598.1|BI807598
EST:     CGAGAGA-CTGAGGGATACTG-CCAATATGAG                         AATGACCCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTA-C
genomic: CGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGA-CCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGC
EST: gi|38480632|gb|CF964721.1|CF964721
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88981185|gb|CI026937.1|CI026937
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|86852434|gb|CI320359.1|CI320359
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88965198|gb|CI009234.1|CI009234
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88995411|gb|CI036986.1|CI036986
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|18386960|gb|BM420158.1|BM420158
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|86415835|gb|CI029846.1|CI029846
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|29687966|gb|CB684241.1|CB684241
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88216352|gb|CI216201.1|CI216201
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|15858218|gb|BI811030.1|BI811030
EST:     AATCAATGAGGAAGCTGGCGAGAGA-CTGAGGGATACTGAC-AATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACCGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88985254|gb|CI006908.1|CI006908
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88215926|gb|CI215775.1|CI215775
EST:     GGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: GGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|11863341|gb|AT003766.1|AT003766
EST:     AATCAATGAGNAAGCTGGCGAGAGAGNTGAGGGATNCTGNCAAATATGAG                         AATG-CCAGTACAAGAGCAAGATGAAACAGTCGGATGANCGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88844108|gb|CI001165.1|CI001165
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATCGAACGGCTGCTAGC
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGAT-GAACGGCTGCTAGC
EST: gi|86829554|gb|CI286745.1|CI286745
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCG
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCG
EST: gi|89178535|gb|CI015240.1|CI015240
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88217343|gb|CI217192.1|CI217192
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88836931|gb|CI008367.1|CI008367
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|25798400|gb|CA754361.1|CA754361
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACNAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|88986549|gb|CI033692.1|CI033692
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCA
EST: gi|15856482|gb|BI809294.1|BI809294
EST:     ATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACACAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGC
genomic: ATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACA-AATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGC
EST: gi|58585983|gb|CF984291.1|CF984291
EST:     AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAG                         AATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGC
genomic: AATCAATGAGGAAGCTGGCGAGAGAGCTGAGGGATACTGACAAATATGAGgtgtgcattc ... tggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatagagcttatgcaattaaccttctcgctctttttctgcttggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCACTGGTGAAGGCGGCCATGGATGTTGTGGTGGCCGTAGGGCTTCTTCAGC
                  aattaac  putative branch site (score: 2)
                        ccttctcgctcttttt  CT-rich tract
                  aattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcattctttcatcatctctgcatcccactggaaactgatgacgattgacgagtacaaattttatagagcttatgcaattaaccttctcgctctttttctgcttggtttgtagAATGACCAGTACAAGAGCAAGATGAAACAGTCGGATGAACGGCTGCTAGCACTGGTGAAGGCGGCCATGGATGTTGTGGTGGCCGTAGGGCTTCTTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG