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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcag

Basic information

species Oryza sativa
transcript LOC_Os01g60960.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacca--ttacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatg-cggtttcag
||| |||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| |||||      ||  ||  ||   ||| | | | ||   |     || | | ||     |       | |  | ||    |    |   ||  |||
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttt---tctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G15050.1 (Glycine max), 5'ss of exon 1
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcag----------------------------------------------------
 || || |||||  | || || ||||| || || ||||| || ||||| ||  | |||||||| ||||| || |||||||||||||| ||||||||| |||||  |||     |||   ||  | |  | | ||    || |  | ||||||| ||   |||||           |  ||   |  |||                                                      
AGAATGTCCCTTTTCTCCATATTTCTCTCCCCATGAGCCTCAAAAGTTTGCTTCTGTCCACAAAGTCTTTGGTGCCAGCAACGTCTCAAAGATGCTCATGgta-aatatacacaca---cacggtacacataaa----taacactagctagctagttatttaattaaccatatcatataacatgtattccacttattatagattttaatcatatcatataatttcttcgacaatgtgttgtag

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G30340.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaagcattccttaaattgtacctttcgctag---cttgtgcattaatggcttcgtcggtgcaatgcggtttcag-------
|||||| || ||| | || |||||||||||||| || || ||||||||||| ||||| || || ||||| || || |||||||||||||||||||| |||||||       ||  |  | || | | |  |||  || |    || | ||     |  |   || ||  ||   | | |    |      | |        
GGAGTGTCCTTTCTCGCCTTACTTCTCGCCGCATGAACCTCACAAGTTCGCTGCCGTTCATAAAGTCTTTGGTGCAAGCAACGTCTCCAAGATGCTTCTGgtacacatattttctacattaatg-aatatttattttcttttcttagttaaggtttcttaatttgattactcttttgatatcgtatttgattaatctgaat

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgta----cgataccattacaggtcaaagcattccttaaattgtacctttcgcta--gcttgtgcattaatggcttcgtcggtgcaatgcggtt-tcag--
 || || |||||  | || || ||||| || |||||||| || ||||||||  |||||||||| ||||| || || || |||||||||||||||||  |||||    | ||  ||  |||     |   ||    |  |||    | | |  ||   | | || |  |||  |    |    | |||   ||  |||   
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaa----gcattccttaaattgtacctttcg-ctagcttgtgcattaatggctt-cgtcggtgcaatgcggtttcag
 |||||||| ||| ||||||| ||||| || || || || |||||||| || || |||||||| || || || |||||||||||||||||||||||| |||||     ||| | |   || ||     || || | | |  || |    |  ||    | | | |  ||   ||  |    | ||||  |       
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatttatgcatatacaattag-------

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0067g02380.t01 (Vitis vinifera), 5'ss of exon 2
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaa----agcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcag
 || ||||||||  | ||||||||||| || || || ||||| ||||| ||  |||| ||||| ||||||||||||||||||||||||||||||||| |||||  |  | | | | |   |     || ||| | |    |  |    | | || ||| |  | |  |    |  |   | ||            
AGAATGCCCCTTTTCTCCCTACTTCTCTCCCCATGAACCCCAGAAGTTTGCTTCCGTTCACAAAGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCATGgtagaaccctaattctgtctaccagtagtatttcatgttcttgattgattgataacttctcaaatcttacactgttaaattcag-----------

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ35900 (Selaginella moellendorffii), 5'ss of exon 1
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatg--cggtttcag---------
 ||||| ||||| || || ||||||||||| |||||||| || ||||| |||||||||||||| || ||||||||||||||||||||||||||||||  ||||||  | || | ||   |    |  | |          ||   | | | ||  | ||||       |    ||| |  |   |  |||| |         
AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaat-catccctcttctcttcccgtggcaatccgagcacca-ctattccattgtctttctaagtggtactcttttctctttcggagtgtgctt

upper sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ09483 (Selaginella moellendorffii), 5'ss of exon 1
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaagcattccttaaattgta-cctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcag---------
 ||||| ||||| || || ||||||||||| |||||||| || ||||| |||||||||||||| || ||||||||||||||||||||||||||||||  ||||||  | || | ||  ||    |    ||      ||  || | ||    |   |     | || |||  |  |||  |  |  ||             
AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaat-catctctcccctcctctcttcccgtggccctccgagcaccactattccattgtctttctaagtggcactcttttctctttcggagtg

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|88226735|gb|CI224720.1|CI224720
EST:     CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTG                         GAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
genomic: CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacc ... gcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
EST: gi|117249598|gb|CT863295.1|CT863295
EST:     CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTG                         GAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
genomic: CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacc ... gcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
EST: gi|88385675|gb|CI566537.1|CI566537
EST:     CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTG                         GAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
genomic: CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacc ... gcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG