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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtactatgctgcttttgctcgttgctatacttgattattttcttctacttcaaaatcgatgtacaatgttaggtgtaaactgtatcatgaacgtaaaatggaagaaaggtgttatcaattgaattgaatcctgacatggttcttgttttcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTGAACAAGGAGCTCTACTGAAGGTCGA

Basic information

species Oryza sativa
transcript LOC_Os08g40170.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G068193_T02 (Zea mays), 3'ss of exon 5
gtttgtactatgctgcttttgctcgttgctatacttgattattttcttctacttcaaaatcgatgt-acaatgttaggtgtaaactgtatcatgaacgtaaaatggaagaaaggtgttatcaattgaattgaatcctgacatggttcttgttt-tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTGAACAAGGAGCTCTACTGAAGGTCGA
                                    |    |  ||    |||    | |  || |  ||  | | |  |   |    | |    |    |  ||  || |||| |||    ||| |     || ||   || | | |||||  ||   |||||||| ||||| | ||||||||| ||||||||||| | |||||||||||| ||||||| ||||||||||| || ||||  ||||            |   ||
------------------------------------gtcagtactcactcactcagcagtgaatctcgcagcggtggtggctgagaagagctaatattatatctgtgaggaaggggttgcatattcat----attct--tattgcttttgttggtctgctgcagAAATTGCTGGAATACGAGCCGGCGAAGCGGATCCCCGCGAAGAAGGCCCTGGAGCACCCCTACTTCAAAGATGTGAGGAAGGGAGATGCGCACTGACTGA

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttgtactatgctgcttttgctcgttgctatacttgattattttcttctacttcaaaatcgatgtacaatgttag-gtgtaaactgtatcatgaacgtaaaatggaagaaaggtgttatcaattgaattgaatcctgacatggttcttgttttcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTGAACAAGGAG--CTCTACTGAAGGTCGA
                                                                |||      ||| || |||      ||    || |    ||      || |   |||| |    |   |  || |  || |  || | || |    |||||||||||| ||||||||||  | || || ||||| || ||||| || ||||||||||| |||||| | ||  ||    |  ||  ||||     |||    
----------------------------------------------------------------gtaagtctctagtgtctaacacacctctcagaccttgcttgattagtagata--atcactctgctgaga--ctaatttg-tgtttctctttgtgcacagAAAATGCTGGAGTACGAGCCAGCAAAACGAATCTCAGCAAAGAAAGCTATGGAGCATCCTTACTTCGATGATTTGCCTGACAAGTCCTCTCTCTGAGGCT--

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G76540.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttgtactatgctgcttttgctcgttgctatacttgattattttcttctacttcaaaatcgatgtacaatgttaggtgtaaactgtatcatgaacgtaaaatggaagaaaggtgttatcaattgaattgaatcctgacatggttcttgttttcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTG--AACAAGGAGCTCTACTGAAGGTCGA
                                                                         || || |||| | ||| |        |  |   | ||     | | ||   ||| | | |        | || |   || |     |||||||||||||||||||||||  |||| || ||||| || |||| ||| ||||||||||| |||||  | ||  ||  |  || |  ||||    ||||    
------------------------------------------------------------------------gtaagtctaaagtttatta-----actagctaccaaaacaaactcaacagacgaactaatt------gcgtttttatcttcctggaacagAAAATGCTGCAGTACGAGCCAGCGAAACGAATCTCAGCAAAGATGGCTATGGAGCATCCTTACTTTGATGATCTGCCAGAAAAGTCCTCTCTCTAAGGAT--

upper sequence: LOC_Os08g40170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ19614 (Selaginella moellendorffii), 3'ss of exon 7
gtttgtactatgctgcttttgctcgttgctatacttgattattttcttctacttcaaaatcgatgtacaatgttaggtgtaaactgtatcatgaacgtaaaatggaagaaaggtgttatcaattgaattgaatcctgacatggttcttgttttcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTGAACAAGGAGCTCTACTGAAGGTCGA
                                                                                           |||   |          | || ||  | |   | |  | | |  | ||||  | | |   |    | ||||||||||||||| ||||| || || |||||||||||||| |||   || ||| | || || |||||| |  || |  |||||  ||  |  | |       
------------------------------------------------------------------------------------------gtgagtttctcgatttctagagatg--aacctcttatctcactttttacatt-tccatccgtcttctcgcagAAAATGCTGCAATACGATCCTTCCAAGCGGATCTCTGCAAAGGCAGCAATGCAACACCCTTACTTCGAAAACCTCGACAAGTCGCAGTTTTAA-------

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|29663133|gb|CB659408.1|CB659408
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|58604123|gb|CK014651.1|CK014651
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGTTGCAGTACGAGCCGTACGAAGCGGATCTCTGCGAAGAAGGCCAT
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGT-CGAAGCGGATCTCTGCGAAGAAGGCCAT
EST: gi|33801905|gb|CF326824.1|CF326824
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTTTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|89175978|gb|CI042999.1|CI042999
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|86421815|gb|CI059388.1|CI059388
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|88962742|gb|CI023842.1|CI023842
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|86496840|gb|CI139473.1|CI139473
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|88961833|gb|CI096986.1|CI096986
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|86593618|gb|CI264497.1|CI264497
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGTTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|88850591|gb|CI094856.1|CI094856
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|58603848|gb|CK014376.1|CK014376
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
EST: gi|88975465|gb|CI023716.1|CI023716
EST:     TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAG                         AAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG
genomic: TGTCTGATCTTGTCCATGGTCTCGACGCTGATGCTCTTGATCTTCTTGAGgtttgtacta ... tcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaggtgttatcaattgaattgaatcctgacatggttcttgttttcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTGAACAAGGAGCTCTACTGAAGGTCGA
                         tcctgac  putative branch site (score: 2)
                                    ttcttgttttc  putative PPT
        ttatcaattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtactatgctgcttttgctcgttgctatacttgattattttcttctacttcaaaatcgatgtacaatgttaggtgtaaactgtatcatgaacgtaaaatggaagaaaggtgttatcaattgaattgaatcctgacatggttcttgttttcgattgcagAAAATGCTGCAGTACGAGCCGTCGAAGCGGATCTCTGCGAAGAAGGCCATGGAGCATCCCTACTTCAACGACGTGAACAAGGAGCTCTACTGAAGGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG