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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

Basic information

species Oryza sativa
transcript LOC_Os02g54340.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
|||| |  |    ||||||       ||  | |   | | | | | ||      || | | ||||     | ||| |||||||||  ||     ||    |    |||||||||||||| |||||||| |||||||| ||||| ||||| |||||||||||||| |||||||| || ||||||||||| || || || |||||||| |
gtatatatatggctgtgaa--tctgtaaatattatcccagtcttttcat-----gtacgtgtgttc----aacatatttctgaaatgaa-----ttcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
                | |||  || |||| | |  |   ||   ||  || |      | |   ||| |  ||    | |||  ||||     || |  |  | |||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||| ||||||||||
----------------gtaaatacataaga-cgtgcc---ttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaat----tttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
              |||| || |  | |  |   |    |||| |  | ||    | |   | |||      |||| ||      ||  |||  || |  |  | ||||||||||| || ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||
--------------gtgagaa-tggctaagatgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
gtatgtgcaacattgtgaa-aactcacaagaacttatcaatt-ttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
              |||||   || | | | || |   | || || |  | ||   ||   | |   ||||| |  |   |||||  ||||     ||||  |  | |||||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||
--------------gtgaatggctaagatgcaccttctatttattttatatttttcgt-tgtttccatgacatgatttcatctgactaaaat----ttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
              || ||||  ||||||| ||  ||   |  ||    || |      | |   ||| ||  |  |   |  |  ||||  |  | | ||   ||||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||| ||||||||||
--------------gt-aaaatgcacaaga-ctcgtcctctagcttttttttatcattgtttccatga-aaataaatcatttgactaaaattttctcattt---ttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
gtatgtgcaacattgtgaa-aactcacaagaacttatcaatt-ttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC------------------
              |||||   || | | | || |   | || || |  | ||   ||   | |   ||||| |  |   |||||  ||||     ||||  |  | |||||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||                  
--------------gtgaatggctaagatgcaccttctatttattttatatttttcgt-tgtttccatgacatgatttcatctgactaaaat----ttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
    |||| |  || |      |      |  | | || |  | | ||  | | ||  ||     |||    |||| | |  ||       |||||   |  |   ||||||| || || ||||| || |||||||| || ||||||||||| |||||||||||||||||||| || || |||||  | |||||||||||||||||||
----gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttga--tgattctcatggtgc--aacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttg-gtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
       |  || ||| |    | ||   |||   | | |  | || | | |  |||      || ||     ||  |  ||  |            ||||| |   |||||||||| || |||||||| |||||||| || ||||||||||| ||||| |||||||||||||| ||||| |||||| | || |||||||| |||||||
------ccgccagtgt-attgtttactcaaacgc-taagtactgtgtattcac-gtggcctacttcgatgcttatcgtggtgcgatttgtttatggaacttgtgagcagATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC

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|58654487|gb|CK043167.1|CK043167
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
EST: gi|84117608|gb|CD151375.1|CD151375
EST:     TCAAAAATATGTTGGTGAAGGGGCGACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTC
genomic: TCAAAAATATGTTGGTGAAGGGGC-ACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTC
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
EST: gi|8857968|gb|AU095286.1|AU095286
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGC
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAA-GCATGCATTGTCTTCTTTGATGAGGTTGATGC
EST: gi|58600395|gb|CK010923.1|CK010923
EST:     TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAG                         ATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT
genomic: TTCAAAAATATGTTGGTGAAGGGGCACGGATGGTCCGGGAATTATTTCAGgtatgtgcaa ... cttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
                                       tgttgac  putative branch site (score: 3)
                       tttctgaaaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG