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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
||| |||    |||| ||| |   | ||  ||    |  |   ||  | |||  ||    |||||     | |  ||||  |||   ||||||||||||||||| |||||||||||||| ||  ||||||||||||||||||||||||| ||||| ||||| |||||| |||| ||||||||||||||||
gtatgatcacttccaattttacattgagctctg--gttggcagttagcacatgatt---aaacac-----atttctctcc-acacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
-------------gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaa-cagtattctc----tgac--attctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
              |   ||| |    | | |   | |      || |       ||| ||    |  ||  |     ||   |  ||||| |    || |  |||  |||||||| | ||||| ||||| |||||||| || || || |||||||||||||| ||||| ||||| || ||    ||  | ||  |||||||||||||||
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
gtaagattggatcc---agtttcaggattagtgctactatcaggcattttcccatcttttatgaacact-gaacagtattctctgacattct-------------agATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
||||   |    ||   | |||      | ||     ||  |   | ||   | | || | |  ||||| |    |  | ||   | |||||             |||||||| | ||||| ||||| |||||||| || ||||| |||||||||||||| ||||| ||||| || ||    ||  | ||  |||| ||||||||||
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
||  | ||        |         | |  ||  | || | |    |       |   |        |  |  ||  |     ||  |||| || ||||| || |||||||||||||| || || ||||||||||||||||||||||| || || ||||| |  ||  | ||  |||| || || ||| 
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
    |   |  ||   ||      | |||      |  || ||  ||   |   || ||     |  || |    ||| |||  ||  || |||| ||||| || |||||||||||||| || || ||||||||||||||||||||||| || ||||||||||| ||  | ||  |||| || || ||  
----gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgt-caaaata----tctttgat-tttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 9
-----gtaagattggatcca-gtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacatt-----ctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
     ||    ||  || ||  || ||   || ||||  || | |   || ||    |      |  |   |   || | |||  |  || |     | |||||||  | ||||| |||||||||||||| || || ||||||||||| ||||| || |||||  | ||||| || ||  ||||  |||| || |||||||
gtatggttctcttttattcacattccaacttttgtgc--cttttaaatatgttgttgtaaggcctttattgtttgcaatgttccttttcaattgataccagATTGTGCTAGAAGCAGATGGTTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCAT

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
----gtaagattggatc---cagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgac---attctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
     ||  ||||  |    | || |||   ||| | |||   |  ||  | ||       | ||   ||  |||    | ||| |  |     |   ||||||| || ||||| |||||||||||||| || || |||||||| |||||||| ||||| || || |||||    || |||||  | ||||| |||||||
gtatctaccattgtgttgttcggtctcaatttta-tactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT

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|29622847|gb|CB627858.1|CB627858
EST:     TTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAAGG                         ATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAA
genomic: TTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAAGGgtaagattgg ... gacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAA
EST: gi|58668422|gb|CK057108.1|CK057108
EST:     TTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAAGG                         ATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAA
genomic: TTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAAGGgtaagattgg ... gacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
                                         ctctgac  putative branch site (score: 3)
                                       ttctctg  CT-rich tract
               atcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG