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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGCTATTTGTGGTACGAGTATATTTACAAACTAGACAAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatagaaatatgccataaaatatatatgtgggcttttgtatcagtgttaatgataccacggtttccatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT2G34410.3 (Arabidopsis thaliana), 5'ss of exon 11
GCTGGCTATTTGTGGTACGAGTATATTTACAAACTAGACAAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatagaaatatgc---cataaaatatatatgtgggcttttgtatcag--tgttaatgataccacggtttccatgcag---------------
| ||| ||  | ||||| || || || ||||| || |||||  ||||||||||||| || ||||| |||||||| |||||||| || |||| |||||  ||    |    | |  |    | |  |     ||||        |  |    | |    |  ||       |               
GTTGGTTACCTATGGTATGAATACATATACAAGCTTGACAAGGTTACATACAACAAATATCATCCCTACACATCGTGGATTCCAATAACgttagtatcaaatcccgttttctttcaccccaaacattaaactttgagatgtcttactctctaaattctgactttagctttgattattttgtcttag

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 5'ss of exon 12
GCTGGCTATTTGTGGTACGAGTATATTTACAAACTAGACAAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgt--gagtatagaaatatgccataa--aatatatatgtggg-cttttgtatcagt-gttaa---tgataccacggtttccatgcag--------------
| ||||||| ||||||| || | ||| ||||| || ||||  |  |  ||||||| ||| |||||||||||||||||||| || |||||||  | | ||| || | |    | |    | | ||| |  | || || | ||| | | | |   ||| ||     |  ||||                  
GTTGGCTATGTGTGGTATGAATGTATCTACAAGCTGGACAGGACCAGTTACAACATGTATCATCCGTACACATCATGGATCCCCATCACgtctgtgcataaaactctttttttattggtctttatatttgtctcttatgtcacttgctgaaactgaaacatgactcaccatttgatttctgggttccag

upper sequence: LOC_Os01g44040.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 5'ss of exon 6
GCTGGCTATTTGTGGTACGAGTATATTTACAAACTAGACAAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtat-agaaatatgccataaaatatatatgtgggcttttgtatcagtgttaatgata--ccacggtt-tccatgcag-------------------------------------------------------------------------------------------------
| ||| ||||||||||| || || |||||||| || |||||| ||||||| || |||| |||||| ||||||||||||||||| || ||||  || | |  | | |  |      | |   | |    | || | ||| | |   ||  |    | ||   |  ||  ||                                                                                                 
GTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAACgtatgtgttaagagtctctctctctctctcactcttctttcttctctcattctctctgtcaatttatggaaatgtattaaggagttctatagtgtggcatgaagaatatcagatctaattgaacattccagtttagtctcagtatctcattatcatctttgttttattgtgattccag

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|86885457|gb|CI318608.1|CI318608
EST:     ACAAG-ACCATCCGTACACATCA-GGATTCCTATCAC                         TGTTTA-ATCT-CCTAAGG-A-TGCACTCAGCAGCGTAGAAACGTCTCTTT
genomic: ACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatag ... ttccatgcagTGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
EST: gi|87006678|gb|CI285712.1|CI285712
EST:     AAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCAC                         TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
genomic: AAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatag ... ttccatgcagTGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
EST: gi|29659100|gb|CB655375.1|CB655375
EST:     AAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCAC                         TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
genomic: AAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatag ... ttccatgcagTGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
EST: gi|89177189|gb|CI043692.1|CI043692
EST:     ACCATCCGTACACATCATGGATTCCTATCAC                         TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
genomic: ACCATCCGTACACATCATGGATTCCTATCACgtgagtatag ... ttccatgcagTGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
EST: gi|86502826|gb|CI145459.1|CI145459
EST:     AAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCAC                         TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
genomic: AAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatag ... ttccatgcagTGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
EST: gi|88956170|gb|CI092458.1|CI092458
EST:     GTACCATCCGTACACATCATGGATTCCTATCAC                         TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT
genomic: GTACCATCCGTACACATCATGGATTCCTATCACgtgagtatag ... ttccatgcagTGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGCTATTTGTGGTACGAGTATATTTACAAACTAGACAAAATTACATACAACAAGTACCATCCGTACACATCATGGATTCCTATCACgtgagtatagaaatatgccataaaatatatatgtgggcttttgtatcagtgttaatgataccacggtttccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA