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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catattatctactgttatgaattgatatctcataacttatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG

Basic information

species Oryza sativa
transcript LOC_Os01g64650.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 5
catattatctactgttatgaattgatat-ctcataacttatttttcatatgggtaaaactgc--ttgctgat-gtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
|||| | | | | | | | | || | ||| | || | | || | | || || ||| |||||| | |||||||| ||||||||||||||||||||||||| || ||||| || ||||||||||||||||||||||| || || || |||||||||||||| |||
----ttatgtgcatactttagtctctgtgcgcaaatctttgaatatatgggaatctgaccacagctactaattgtgggccctttatgatttaatattttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG

upper sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 4
catattatctactgttatgaattgatatctcataacttatttttcatatggg----taaaactgcttgctga-tgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
|||| | | | | | | | || | || ||||||| | | | ||||| | |||| | |||||| | |||||||| |||||||||||||||||| ||||| || ||||| || ||||||||||||||||||||||| ||||| || || ||||||||||| |||
----ttatgtgcatactttagtctgtg-cgagcaaatctttgaatatatgggaatctgacaacaattgctaactgtgggtcctttatgctgtaatattttcacagCATAAAACTATTGATAGTGTCCTGGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGTTCTGATCTAAGTGCTGCTTCTCAG

upper sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
-catatt-atctactgttatg-aattgatatctcataact---tatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
| || || | | || ||||| | | | | ||||| || ||| | | || | || | ||| |||| | | ||||||||||||||||||| |||||||| |||||||| | ||||||| || |||||||||||||| || |||||||| ||||| |||
ttttgttcatttcttcctacacaattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtt------tataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG

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|87005252|gb|CI283475.1|CI283475
EST:     AAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATTAAAACNTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCT
genomic: AAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCA-TAAAAC-TATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCT
EST: gi|89197611|gb|CI012392.1|CI012392
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACCAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86601691|gb|CI256196.1|CI256196
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|218482998|gb|FG956126.1|FG956126
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88230905|gb|CI228810.1|CI228810
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86484196|gb|CI126829.1|CI126829
EST:     TGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: TGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86424480|gb|CI063241.1|CI063241
EST:     AGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: AGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88212458|gb|CI212098.1|CI212098
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88967922|gb|CI098164.1|CI098164
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATNGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88237358|gb|CI237207.1|CI237207
EST:     AAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: AAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|38468730|gb|CF952861.1|CF952861
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88243877|gb|CI242999.1|CI242999
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|89189985|gb|CI013552.1|CI013552
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|218479888|gb|FG958307.1|FG958307
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88962198|gb|CI097351.1|CI097351
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88838962|gb|CI012838.1|CI012838
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACCAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86541854|gb|CI182060.1|CI182060
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86541898|gb|CI182104.1|CI182104
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88252245|gb|CI350673.1|CI350673
EST:     GACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: GACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88237346|gb|CI237195.1|CI237195
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88274492|gb|CI394898.1|CI394898
EST:     ACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86542456|gb|CI182662.1|CI182662
EST:     TAATGAAAATCCAGAGGGACTTGGATGAAACCAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: TAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88844006|gb|CI008587.1|CI008587
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88963812|gb|CI031145.1|CI031145
EST:     GTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: GTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88985416|gb|CI002933.1|CI002933
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACTAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88975339|gb|CI023590.1|CI023590
EST:     AGAGGGACTTGGATGAAACAAAAATTACCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: AGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86507385|gb|CI150018.1|CI150018
EST:     AAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: AAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88850613|gb|CI094878.1|CI094878
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATNGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88833199|gb|CI076682.1|CI076682
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88847504|gb|CI015997.1|CI015997
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|88240976|gb|CI240825.1|CI240825
EST:     AAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGGGGGGAAAGATTGGATAGCTTG
genomic: AAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86416630|gb|CI030641.1|CI030641
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST: gi|86594435|gb|CI253334.1|CI253334
EST:     ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA                         CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG

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: 66 (upstream exon), 74 (downstream exon)
Score: 82

GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
                                      ttctaat  putative branch site (score: 82)
 attgtttatgttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catattatctactgttatgaattgatatctcataacttatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - -tactgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt