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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag

Basic information

species Oryza sativa
transcript LOC_Os01g23740.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 2
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag
|||||||||||||||||||||||| |||||||||||||  |||||||||||||| |||||||| ||||||||||| ||||| ||||||| |           ||| |||  |   |  ||   | |      ||||   |||||  |   ||    || |||||   |  | ||| | |   ||   | |     | ||  |                                                                            
GTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAGgtatatgt---------atatctgtcatacacatgaagaatt-----aaattggttctctacctgatgaatct-ctcagcattacttagatatta--tatgtccttttattccacta----------------------------------------------------------------------------

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 2
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag
|||||| |||||||| |||||||| || || |||||||||||||||   || |||||||||||||||||||| || || |  |||||  |  |    ||    |  ||   ||   || |   | || || | ||| ||||||  |  |  |     |  |  | |||  |    || |  ||    |||                                                                                        
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAGgtcagcaccttggt---gtttctttcaaaatttcgaataatgttttacaat-ttttctgtttactttatattttttttgtggtattttttaagt--ttcaggcatt---------------------------------------------------------------------------------------

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 3
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcag-aggtggtcagaaaatggttagaacat-gcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag
|||||| |||||||| |||||||| || || |||||||||||||||   || |||||||||||||||||||| || ||||  |||||  |  |            |||| |  || |||  | |   ||  | | ||||||  ||| |   ||    |||| |  |  | ||      ||  || || | |     |||                                                                                 
GTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAGgtcagcac------------cctggtgtttctttcagaacctct-aatattattttaccatttt--tctgtttacttaataatttgttgtggtattttttgagcttcaggcattt--------------------------------------------------------------------------------

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 5'ss of exon 2
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttc---tcaagttcaatacctg---ctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag
|||||||||||||||||| ||||| || |||||||||||||| || ||||| |||||||| || || ||||| || |||||||||||  ||     || | |||  ||       | |||  ||     || | |  |  |||  || |     |     |  |     || |                                                                                                               
GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGgttagtgtgattctatttcggtattcagctccaatgtttaaaagatagatgaatgatagattgtttcaacttgtgtattgtggtgaag---------------------------------------------------------------------------------------------------------------

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|88354765|gb|CI614043.1|CI614043
EST:     AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG                         GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG
genomic: AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctc ... ctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG
EST: gi|58598802|gb|CK009330.1|CK009330
EST:     AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG                         GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG
genomic: AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctc ... ctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG