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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcatttaatttttactcttggctttatcattatgcaacataaagtaatatgtttaagactcctttgtgttcaattggttggaccatgctcc...

Basic information

species Oryza sativa
transcript LOC_Os03g52340.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G108115_T01 (Zea mays), 5'ss of exon 8
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcattt----aatttttactcttggctttatcattatgcaacataaagtaatatgtttaagactcctttgtgttcaattggttggaccatgctcc
 |||||||| ||| | ||||||||||||||||||| |||||| || |||||| |||| |||||||||||||||||||| || | |||| |||||||  ||||| |||   | |||    |||  | | |   |    || |||  |   |  | |    |||           ||    |  | |  || ||      || || 
CGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGATGGGGACAGCCATATGAATCAGCCAgtatgtagtccgtttctcaaatactcattaccgctcctaccatattatgatttgaga-gatactccctccgtcccaaaataatga--tgctttaggtttgttc-

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G521844_T01 (Zea mays), 5'ss of exon 8
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcatttaatttttactcttggctttatcattatgcaacataaagtaatatgtt-taagactcctttgtgttcaattggttggaccatgctcc
 |||||||| ||| | ||||||||||||||||||||||| || || |||||  |||| ||||||||||| ||||||||||| | ||||||||||||  | ||| |||   ||| |      |||||    ||     |||||| | |  | ||  ||||| | | |   |  || |  ||   | |         || |  
CGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCTTGGCCTTGGAACTGCTCTGAAAATTCTTTTCTCCGTTGATGGAGACAGCCATTTGAATCAGCCGgtatgtagtccatctctcaaatactcactcctgccatattatg-atctaagagatatatgctgttaattttgttggcatttgctcgaaaactgtttgtttt

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA09G10830.2 (Glycine max), 5'ss of exon 8
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtat--ctcatttaatttttactcttggctttatcatta-tgcaacataaagtaatatgtttaagactcctttgtgttca-attggttggaccatgctcc
|||||| |||||||||||||| || || || |||||||||||||| |||||||| |||||||| ||||||||||||||  |  |  | | || |||  ||||| |||    |   || |  |||  |  |     | ||  || |||  | |  |   || |     | |     |||  |    | || |      ||     
TGAGAAATGTCGATTATGGGGCAAACTTCAGGTTCTTGGTCTCGGAACTGCATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacactttgcttgagatttttttgtcttcctctctctactgctgcctttatgcatgtaccataaatcatattgcttctgcagtgatctttaaata----

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G23150.1 (Glycine max), 5'ss of exon 8
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgta--tctcatttaatttttactcttggctttatcatta-tgcaacataaagtaatatgtttaagactcctttgtgttca-attggttggaccatgctcc
|||||| |||||||||||||| ||||| || ||||||||||| || |||||||| |||||||| ||||||||||||||  |  |  | | || |||  ||||| |||  | |   || |  |||     |     | || ||| |||    |  |   || ||    | |     |||  |    | || |      ||     
TGAGAAATGTCGATTATGGGGTAAGCTTCAGGTTCTTGGTCTTGGAACTGCATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacattttgcttgagatttttgtgtcttcctctctttactgctgtctttatgcatgtgccataaatcagattgcttctgcagtgatctttaaata----

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G38960.2 (Arabidopsis thaliana), 5'ss of exon 8
--------TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcatttaatttttactcttggctttatcattatgcaacataaagtaatatgtttaagactcctttgtgttcaattggttggaccatgctcc
        |||||| || ||  ||||||||||||| ||  |||| |||||||||||||||||||| ||||| ||| ||||  |||| ||  || |||||  |||    || ||| ||| |   |  |          || || ||  | |||| | |   ||| | | ||||||  ||  ||| |  |      ||     |||    
GTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAATGGTGAAGACAATTTGCgtcataatgtgcgtttctaacacacctggagac----gcattgtccatttgcaccgt---gtattttctttaagcgtctattgggaacggc-attttagtgatgtag-

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G38960.3 (Arabidopsis thaliana), 5'ss of exon 8
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcatttaatttttactcttggctttatcattatgcaacataaagtaatatgtttaagactcctttgtgttcaa----ttggt--tggaccatgctcc---------------
|||||| || ||  ||||||||||||| ||  |||| |||||||||||||||||||| ||||| ||| ||||  |||| ||  || |||||  |||    || ||| ||| |   |  |          || || ||  | |||| | |   ||| | | ||||||  ||  ||| |  |      || ||  || | ||  ||                 
TGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAATGGTGAAGACAATTTGCGTCATAATgtgcgtttctaacacacctggagac----gcattgtccatttgcaccgt---gtattttctttaagcgtctattgggaacggcattttagtgatgtagcaatctttgttgttttgtttcag

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 5'ss of exon 8
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcatttaatttttactcttggctttatcattatgcaacataaagtaata--tgtttaagactcctttgtgttcaattggttggaccatgctcc
||||||||||||| | ||||||||||| || |||| |||||| || ||||||||||| || ||||||||| |||||||  |  |||  |||   || || ||| || | | |  |    || |    |   ||| |  || | |       || |||   |  ||||     |  ||||  |   |    |||  || | | 
TGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGATGGTCAAGACCTCTTGGGACAGTCTgtaagtttattaaattgacttcaaatataaattttttgttctccttttactagcaattcttacttaatgtgtcactgtgcccctataagaggat-atccac-

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|88539718|gb|CI469698.1|CI469698
EST:     GAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: GAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|29619060|gb|CB624072.1|CB624072
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|58593304|gb|CF991612.1|CF991612
EST:     CATTGAAGATTCGTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|58606099|gb|CK034132.1|CK034132
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCGTTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|88485242|gb|CI422513.1|CI422513
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|86500373|gb|CI143006.1|CI143006
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|88472627|gb|CI409898.1|CI409898
EST:     CATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|29657857|gb|CB654132.1|CB654132
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|33679109|gb|CF307348.1|CF307348
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatctcatttaatttttactcttggctttatcattatgcaacataaagtaatatgtttaagactcctttgtgttcaattggttggaccatgctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA