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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct...

Basic information

species Oryza sativa
transcript LOC_Os03g62640.5
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggtta--atttggtgggtaagcgct--------
||||||||||||   |||||| |||||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||| | ||      | |     |   | |         |   |||   ||   |  ||||   ||||     | |||  | |  || |  ||| | | ||          
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgtttacccc-----ctgatgtttg-----gtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct---
||||||||||||   |||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||||||| | ||     || |   |       |      || |   | | | ||  |  | ||     | |     |      ||| |||  ||  ||         
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgtttctcccctgacgtttcgttgg--aattttggttaggttttaccat-ttcgaaatatgaaattatctatttagttttttgaatatttatctat

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct
 ||||||||||| || || ||||  |||||||||||||| ||||||||||| || |||| ||||| ||| |||||||| ||||| ||||||||| | |||||| | |    ||||    |   || |   |  || ||    |   |||||  | | || ||| ||| ||         |   |||   |  | ||    
TAACGGCGACGTCCGTGAAGTCAATCGCAAGTACTACGATCGCGACGTCTGTCGTCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttttcttccgttttctcactcctcgttcttcgtt-tagggcttcatttttttatttatttattccctttttctctgtttc-cgtttcag----

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct
 ||||||||||| || || ||||  |||||||||||||| ||||||||||| ||||||| ||||| ||| |||||||| ||||| ||||||||| | |||||| | |    ||||    |   || |   |  || ||    |   |||||  | | |||||  || | ||       ||     |    |         
TAACGGCGACGTCCGTGAAGTCAATCGCAAGTACTACGATCGCGACGTCTGTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttttcttccgttttctcactcctcgttcttcgtt-tagggcttcattatttttttgattccctttctctctgtctccgtttcag---------

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcc-----cccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct
 ||||||||||| |||||||| |   | |||||||||||||| || || || ||||||||| | | |||||| ||||| ||||| ||||||||| | |||||||  | |     |  | |||  |  |  | |||   |  | ||  |     |    | |||||  || |       | | ||  || | || ||  ||     
AAACGGCGACGTCCGGGAGGTGAATAGGAAGTACTACGACCGAGATGTGTGTCGCCTCTTCTTGGTCGGCCTTTGCCCTCACGAGCTCTTCCAGTTGACGgtactgttctgggactatcctccttgccttg-atctgttggtttctttagcattggagtctgtttggttctcgagaaagtgtgggaaagtggggggaaaaa----

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ22509 (Selaginella moellendorffii), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct
||||||||| || | ||| ||    ||||||| || ||| || || ||||| ||||||| ||| || |||||||| || ||||| ||||||||||||||||||            |||      || |||||  || | | | |||| |    ||  | |  |||| |   |                            
CAACGGCGATGTCCAGGAAGTGCAGCGCAAGTTCTCCGATCGGGATGTCTGTCGCCTCTACCTTGCTGGCCTCTGTCCTCACGATCTCTTCCAGCTCACGgtaa-----------tcatcgattagaatcca--cagcgcta-gatgttat--tgcatctggttttccacag----------------------------

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ11722 (Selaginella moellendorffii), 5'ss of exon 1
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct
||||||||| || | ||| ||    ||||||| || ||| || || ||||| ||||||| ||| || |||||||| || ||||| ||||||||||||||||||            |||     ||| |||||  || | | | |||| |    ||  | |  |||| |   |                            
CAACGGCGATGTCCAGGAAGTGCAGCGCAAGTTCTCCGATCGGGATGTCTGTCGCCTCTACCTTGCTGGCCTCTGTCCTCACGATCTCTTCCAGCTCACGgtaa-----------tcatcgatcagaatcca--cagcgcta-gatgttat--tgcatctggttttccacag----------------------------

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|29681220|gb|CB677495.1|CB677495
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88692989|gb|CI736564.1|CI736564
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88454050|gb|CI691097.1|CI691097
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATCCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88386151|gb|CI570786.1|CI570786
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88695522|gb|CI737560.1|CI737560
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88724607|gb|CI747866.1|CI747866
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88692917|gb|CI736492.1|CI736492
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCACTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88735255|gb|CI758763.1|CI758763
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTG
EST: gi|88745532|gb|CI768892.1|CI768892
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88591376|gb|CI707406.1|CI707406
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
EST: gi|88717451|gb|CI740961.1|CI740961
EST:     GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCACCTCACG                         AAAATGGATCTCGGGCCTTGCCCNCAAAGTTCATTCGCCGCACCCTACGGA
genomic: GCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCC-CAAAGTTCATTCGCTGCAGC-TACGGA
EST: gi|88730423|gb|CI754036.1|CI754036
EST:     CCGCCTCTTCCTCGCCGGCCTCTGCCCCCNA-GACCTCTTCCAGCTCACG                         AAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG
genomic: CCGCCTCTTCCTCGCCGGCCTCTGCCCCC-ACGACCTCTTCCAGCTCACGgtaccttccc ... ttcatggcagAAAATGGATCTCGGGCCTTGCCCCAAAGTTCATTCGCTGCAGCTACGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA