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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTACAGCTGGTCATAGTAGGGTAAAGAAGTTGCTCGCCTGTAAGCACAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattgtgagatcccattcaccttttccttttttgaggagcactgcattgatggcactcatattcaaacctgcttactctattcttacttgagttcgttgatcctgctag

Basic information

species Oryza sativa
transcript LOC_Os03g16700.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G110309_T01 (Zea mays), 5'ss of exon 3
AATTGTACAGCTGGTCATAGTAGGGTAAAGAAGTTGCTCGCCTGTAAGCACAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattgtgagatccca--ttcaccttttccttt--tttgaggagcactgcattgatggcactcatattcaaacctgcttactctattcttacttgagttcgttgatcctgctag
|||||||||||||   |||||||||||| |||||||||| || ||||| ||||||||||||||||||| ||| |  |||||   |||||||||||||||||| |||| ||  | |||     ||  ||||||| |||  |||  | | |||| ||||||||| | |  ||| ||| ||  ||   | ||     ||||||  || ||| |||    ||
AATTGTACAGCTGAGTATAGTAGGGTAAGGAAGTTGCTCACCAGTAAGTACAGGAAAGTTGCTCCAGCGAGGGTTTACAAATCTGATCTTTCCTATAGTGgtaagcactggaaaatcttgatttttccttttcttttaatttctgtaacactacattgatggaatttgtatccaagccaactccatgta-----acttgaactcattggtcccatcag

upper sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G063151_T01 (Zea mays), 5'ss of exon 2
AATTGTACAGCTGGTCATAGTAGGGTAAAGAAGTTGCTCGCCTGTAAGCACAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattgtgagatccc--attcaccttttccttt--tttgaggagcactgcattgatggcactcatattcaaacctgcttactctattcttacttgagttcgttgatcctgctag
||||||| |||||   ||| |||||||| |||| ||||| |  ||||||||||||||||||||||||| ||||| ||||||   |||||||||||||||||||||||  |  | |  |   |||   |||||| |||  ||| || | |||| ||||| ||| | |  |||||||||| |||   | ||     |||||| ||| |||||||    ||
AATTGTAAAGCTGAGTATAATAGGGTAAGGAAGCTGCTCACTAGTAAGCACAGGAAAGTTGCTCCAGCGAGGATTCACAAATCTGATCTTTCCTATAGTGgtgagcacaggaaaaatcttgatttttcttttcttttcatttcagtaacactacattggtggaatttgtattcaaaccagctccatgta-----acttgaattcattgatcccatcag
















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|88448616|gb|CI694007.1|CI694007
EST:     CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTG                         ATGTTGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATACACGAC
genomic: CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattg ... atcctgctagATGTTGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATACACGAC
EST: gi|163926542|gb|EG712406.1|EG712406
EST:     CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTG                         ATGTTGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATACAC
genomic: CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattg ... atcctgctagATGTTGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATACAC
EST: gi|29630486|gb|CB635495.1|CB635495
EST:     CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTG                         ATGTTGACCGGAAGCCTTCTTTCCGCA-CAAGAAAATGTATTATA
genomic: CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattg ... atcctgctagATGTTGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATA
EST: gi|29627240|gb|CB632251.1|CB632251
EST:     AGGAAAAGT-GCTCCAGCCAGGATGCACAAAAGAGATCTTTCCTATAGTG                         ATGTTGACCGGAAGCCTTCTTTCCGC
genomic: AGGAAA-GTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattg ... atcctgctagATGTTGACCGGAAGCCTTCTTTCCGC
EST: gi|218487578|gb|FG960601.1|FG960601
EST:     CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTG                         ATGTAGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATACACGAC
genomic: CAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattg ... atcctgctagATGTTGACCGGAAGCCTTCTTTCCGCAACAAGAAAATGTATTATACACGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTACAGCTGGTCATAGTAGGGTAAAGAAGTTGCTCGCCTGTAAGCACAGGAAAGTTGCTCCAGCCAGGATGCACAAAGGAGATCTTTCCTATAGTGgtgagcattgtgagatcccattcaccttttccttttttgaggagcactgcattgatggcactcatattcaaacctgcttactctattcttacttgagttcgttgatcctgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC