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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaagAGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAA

Basic information

species Oryza sativa
transcript LOC_Os02g58730.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 2
gttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaata--aataaaaatttgacaaatttaacaggacaagAGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAA
         || | ||| ||        ||||    |  | || || |||       |||| |  | ||   |  | |  ||   | |||  |  | |||   ||||||||| || |||||||| || || ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||||||      
--------gtctcttcccttg-------gcattaaaatccttctttgtatctgcattccttcc-tgctccaaagtacagtaactgatattctatgatttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGT------

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 4
gttctactttcccctccttttaatggatgcatgcgtaaacctccttatatac-atccacctttcacggtcatcaaaataaataaaaatttgaca-aatttaacaggacaagAGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAA
                         | ||    | |  |  |  || | |         | | | |   ||   |   |  |     ||||||    |  |||||| ||||||||||||||||| ||| | || ||||||||||| || || ||||| ||| | || || || || ||  |||||||||| |||||||| |||||      
---------------------gcaagttgttaccttggatttttttgtcttttgaatttcctcctcttccagagagtcatttgtgtttttgacttggtgaaacagGGCAAGAGGACTACAATAGACTAAGACCTTTGAGCTATCGCGGTGCAGATGTCTTCTTACTTGCATTCTCACTTGTCAGCAAAGCTAGCTATGAAAATGT------
















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|86900291|gb|CI296334.1|CI296334
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|86900291|gb|CI296334.1|CI296334
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|3763167|gb|AU029919.1|AU029919
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGGACAAG                    
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGAT--A-CA-G-C-AGgttctacttt ... acagg
EST: gi|88718274|gb|CI741363.1|CI741363
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88718274|gb|CI741363.1|CI741363
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88314827|gb|CI608286.1|CI608286
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88314827|gb|CI608286.1|CI608286
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGGACAAG                    
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGAT--A-CA-G-C-AGgttctacttt ... acagg
EST: gi|88406286|gb|CI596413.1|CI596413
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88406286|gb|CI596413.1|CI596413
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGGGGGATACAGCAGGACAAG                    
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGAT--A-CA-G-C-AGgttctacttt ... acagg
EST: gi|88410858|gb|CI578664.1|CI578664
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGAAG                         AGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCC
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaagAGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCC
EST: gi|88725691|gb|CI748950.1|CI748950
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88725691|gb|CI748950.1|CI748950
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGGACAAG                    
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGAT--A-CA-G-C-AGgttctacttt ... acagg
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88693672|gb|CI737247.1|CI737247
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88693672|gb|CI737247.1|CI737247
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88368345|gb|CI577616.1|CI577616
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88368345|gb|CI577616.1|CI577616
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88406839|gb|CI578367.1|CI578367
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88406839|gb|CI578367.1|CI578367
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88363065|gb|CI616222.1|CI616222
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|88363065|gb|CI616222.1|CI616222
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG                         G
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctacttt ... acaggacaag-
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGGACAAG                    
genomic: TGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGAT--A-CA-G-C-AGgttctacttt ... acagg


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaagAGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAA
                                        atttaac  putative branch site (score: 3)
             tcatcaaaataaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaagAGGACTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT