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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttattattctgtctttttctcaattctggttgttgcatgtttagtctatttcaggttgcattattaataatagcccattacattc...

Basic information

species Oryza sativa
transcript LOC_Os03g02756.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 4
TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttattattctgtctttttctcaatt--ctggttgttgcatgtttagtctatttcaggttgcattattaataatagcccattacattc
||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||   ||||||||||||||||||||| |||||||||    || || | ||| || |||| |       |   ||  || ||  ||     | ||||  |  ||    ||    |||   |       | | ||   
TATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAGGATATATATGCAGgttaaacttgtagtctttttcttcttttcccaattattttggcttgtctttaagattgtagtgcagatcttactgatgcatttgcatctatgaactgcag--

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 41
TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttattattctgtctttttctcaattctggttgttgcatgtttagtctatttcaggttgcatt--attaat--aatagcccattacattc
||||| ||||| ||||||||||||||||| || || |||||  | ||||| || || ||||| |||||||| ||||| || ||||| ||||| ||| |||||| ||||  ||   ||  |     ||  ||||     ||||||| |  |   |   |     |   |  | ||| |  | ||||  |    || ||   |   
TATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAAGATATCTATTCAGgtatggctgttgcttttgctgcatagttattttgctg-ttctggt-gcaggggggcaaaatgctgcaaattcgcaatcaagtaatttagctaccaatcctac--

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G44150.2 (Glycine max), 5'ss of exon 39
TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttattattctgtctttttctcaattctggttgttgcatgtttagtctatttcaggttgcattattaataatagcccattacattc---
||||| ||||| ||||||||||||||||| || ||  ||||  | ||||| || || ||||| |||||||| ||||| || ||||| ||||| ||| |||||| ||||  ||   ||  |     |   ||||     ||||||||   |   |   | |   |   |  ||||| |   | ||||    |     || |   
TATGGGCATCCTGATGTTTTTGATAGAATATTCCACGTAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAAGATATCTATTCAGgtatggctgttgcttttgctgcatagaaattttgctt-ttctggttcaggggggcaaaatgc-tgcaaatttgcaat-ccagtaatttagctaccaatcctac

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 5'ss of exon 38
TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttattattctgtctttttctcaatt-ctggttgttgcatgtttagtctatttcaggttgcattattaataatagcccattacattc------------------------------------------------------------
||||| ||||||||||| ||||| ||| | |||||||| ||  | ||||| || || |||||||| || ||||||||||| ||||| ||||| | ||| ||||    |  |    | |||   | ||    |||  || |  | | ||||  | |  ||    |   || |    || |  | |   |  |     ||||                                                             
TATGGTCATCCAGATGTCTTTGACAGAGTATTTCATATTACACGTGGTGGTATCAGCAAGGCCTCTCGGGTCATCAATATTAGTGAAGATATATTTGCTGgtaaatttgattttttaattga-cagttaccttcaaaactgttcgatgttttaagaatataaaaacacatgaataatgaaaagtgcaattctgagccattttttaataccaatttcttccacacatgatggacgttgattatatgcctctacggtttccag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 36
TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttatta--ttctgtctttttctcaattctggttgttgcatgtttagtctatttcaggttgcattattaataatagcccattacattc
||||||||||||||||||||||||||| |||| ||||||||  | ||||| || || |||||||| || || ||||| || ||||| ||||| ||||| |||| |  |  |  ||| || |  | |  |  |  |   |  | | ||||||   |||   || ||||||  |     ||  |  | || ||   | |||   
TATGGCCATCCAGATGTTTTTGATAGAGTTTTCCATATAACACGAGGTGGTATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAAGATATATATGCTGgtatgattgttttcctaataaaatgccattataattgaatattttgttgttatttgtcaggtttatttcctgcatattttgttctcat-gctggtgacaca-

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|29615116|gb|CB620129.1|CB620129
EST:     GTAAGGCCTCCCCTGTCATCAATATCAGTGAGGATATTTATGCAG                         GGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATGTTC
genomic: GTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctag ... tgaactccagGGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC
EST: gi|300216075|gb|HO088701.1|HO088701
EST:     AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAG                         GGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATGTTC
genomic: AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctag ... tgaactccagGGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC
EST: gi|88399969|gb|CI588273.1|CI588273
EST:     AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAG                         GGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC
genomic: AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctag ... tgaactccagGGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC
EST: gi|33679231|gb|CF307470.1|CF307470
EST:     AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAG                         GGTTCAACTCAACTCTGCGCTTANGGAACATAACTCATCATGAATATATTC
genomic: AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctag ... tgaactccagGGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC
EST: gi|29675246|gb|CB671521.1|CB671521
EST:     AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAG                         GGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC
genomic: AATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctag ... tgaactccagGGTTCAACTCAACTCTGCGCTTAGGGAACATAACTCATCATGAATATATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAGGATATTTATGCAGgtagggctagtggccttattattctgtctttttctcaattctggttgttgcatgtttagtctatttcaggttgcattattaataatagcccattacattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT