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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g58730.2
intron # 1
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 1
lower sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 1
tcgttttgtgcgaaaaaataaatctaatgtat-tgcatctttgcatttttaattggcagactgtatgtttaatgggacatttc---ttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
         |  ||  ||     | |  || | | | | |  |   | ||   |   | | | |    ||  |      |        |||||| ||| | |||||||||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||| ||||||||  |||||||||||||||
----ccacagacaactaacgggacgagggtttgttcgtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 3
--tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
  |  | |||  |     ||| | ||| |   |  |  |      | |||   |  | ||| | | |   | |||    | |      | ||||||| |||||| ||||| |||||||| || ||||| |||||||| |||||  | || ||||| | |||| | |||||||| ||||||||||| ||||
aatgttgttgatctgtttaatga-tcttagaaagagtgttaggtaactttctgtaaggagattttgtagctgatgttttagtggaat-tttctatgtgacagGATTATGTGCCAACTGTGTTCGATAATTTCAGTGCCAATGTGATTGTTGATGGCAACACTATCAACTTGGGATTGTGGGATACTGCAG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 3'ss of exon 1
--tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgt-atgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
     |   | || |  | ||  |  | |   |  || ||| |          ||     ||| | | | |        ||  |   | |     | |  ||||| || ||||| || || ||||| |||||||| |||||||| ||||||||||| |  || || ||| | ||||| |||||||||||||
agggatggcgcgcaaggagatgtactttac-cacagcgtctgttagacagcgcttcttgtactcttacgatgtcctaagcacatgcccgttc--gtttcgcagGATTACGTTCCTACCGTGTTTGACAACTTCAGCGCAAATGTAGTGGTCGATGGAAATACCGTCAACCTCGGGTTATGGGATACAGCAG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 1
-tcgttttgtgcgaaaaaataaatcta-atgtat-tgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
  || | ||   | | | ||| || || || ||| |  ||| ||   || ||| ||       |   ||  | |     ||    || |||  ||| || ||||| || ||||| || ||||||||||||||||| || ||||| || |||||||| | |||||| ||| | ||  | |||||||||||||
aacgctgtg-atgtatatatatatatatatatatatatatccttttcttattatttaat--ttttcctgggtgacatctcaagagttaatccttattttgcagGATTACGTTCCTACCGTTTTTGATAACTTCAGCGCGAATGTCGTTGTCGATGGAAACACTGTAAACCTTGGACTATGGGATACAGCAG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ04304 (Selaginella moellendorffii), 3'ss of exon 1
tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
                               |   || ||| | | | |       |||  | |  | |||  |   || |||           || |||||||| || || || || ||||||||||| ||||| |||||||| || ||||| | ||||||||| |||||  | ||||| || || |
------------------------------gtgagattttttcttctctt-----tagatgggaattctaaccgtgaatgtctg---------attccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
                        | |  | | |  | | | | ||  |  ||  |  ||| | | |    |||||   ||| |||          |||||| || ||||| |||||||||||||||||||| || ||||| || |||||||| | |||||| ||| | ||| | ||||| || || |
-----------------------gtgagatttcgt-tttgttctttcctttttctctaactctct-tgggctgggatcgttcatca----------acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|3763167|gb|AU029919.1|AU029919
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88718274|gb|CI741363.1|CI741363
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88314827|gb|CI608286.1|CI608286
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCGGATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|163929269|gb|EG711030.1|EG711030
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88406286|gb|CI596413.1|CI596413
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|58604410|gb|CK014938.1|CK014938
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAAATGTTGTGGTCGA
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAA-TGTTGTGGTCGA
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88410858|gb|CI578664.1|CI578664
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88725691|gb|CI748950.1|CI748950
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88693672|gb|CI737247.1|CI737247
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88368345|gb|CI577616.1|CI577616
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88406839|gb|CI578367.1|CI578367
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACCTTCAGTGCAAATGTTGTGGTCGA
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAAC-TTCAGTGCAAATGTTGTGGTCGA
EST: gi|88363065|gb|CI616222.1|CI616222
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACG                         GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT
genomic: TGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGAT

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: 68 (upstream exon), 75 (downstream exon)
Score: 44

GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGCGCCGTGGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACGgtaggcaatc ... tatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
                               catttcttcatctct  CT-rich tract
                 tatgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - tttgtgc
- - - - - -gaaaaaa
- - - - - - - - - - - - - - -tattgca
- - - - - - - - - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatg