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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAATGGTGAATCAGAAGCCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattttcaaatgttattaagtcttcatgttcttccatgtttctgaacaaagacaggaagacctaacactgctctatacattttcatgtgttcatgtcaatgaag

Basic information

species Oryza sativa
transcript LOC_Os02g03060.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G174596_T02 (Zea mays), 5'ss of exon 6
TTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAATGGTGAATCAGAAGCCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattttcaaatgtta-ttaagtcttcatgttcttccatgtttctgaacaaagacaggaagacctaacactgctctatacattttcatgtgttcatgtcaatgaag
||||  |||||||||||||||||||||| |||||||||||||| |||||| | || |||||||| || |||||||| ||||| || |||||||||||||||||||| ||| ||| ||||  || |  |||||  |  ||   ||  | |   ||       ||    ||   ||   |  |                             
TTGATGTGTGGTCAGTTGGTTGCATTTTCGCTGAAATGGTGAACCAGAAGGCGCTTTTTCCTGGCGACTCTGAGATCGATGAGCTGTTTAAGATTTTCAGgtctta-tttacaagtgttggttcaaacttcaattagtttgttgcatgttg-catgtttgagattctcttctaccaatgcag----------------------------

upper sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 5'ss of exon 6
TTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAATGGTGAATCAGAAGCCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattttcaaatgttattaagtcttcatgttcttccatgtttctgaa---caaagacagg------aagacctaacactgctctat----acattttca-tgtgtt----catgtcaatgaag---------------------------------------------------------------------------
|||| || ||||| || || ||||| |||||||| ||| | |  || |||||  ||||||||||||| || ||||||||| ||||||| ||||||||||||| ||||||   ||   ||    ||||   || ||| || || | |   ||   |||||||  |      | ||  | |||  |   | |    |||||||||   || |    ||| |    ||||                                                                           
TTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGATGATCAGCCAAAAGCCCTTATTTCCTGGAGACTCCGAGATTGATCAACTCTTCAAGATTTTCAGgt-ttaattgctaac--ttccccagtcca-atattcctctatatattacaagtgcaaagacttgtctgcaatgatatcacaagggattgtggaaacattttcaacttgatatcacattttggagaagtagtaaaggacacagaaattgaattgttaactgattataaatctgttactgccttgttttgttgtcttcttctag

upper sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S281_23V6.1 (Physcomitrella patens), 5'ss of exon 6
TTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAATGGTGAATCAGAAGCCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattttcaaatgttattaagtcttcatgttcttccatgtttctgaacaaagacaggaagacctaacactgctctatacattttcatgtgttcatgtcaatgaag
| ||| | ||||| ||||| ||||| || ||||||||||||| ||| | ||| || || ||||| ||||| |||||||||||  | || |  || ||||||| |  | | |  |||  |      | |||| |    | |   |  |||   |  | ||  |   | |   | |     |        ||| |    |     ||||| 
TAGACGTCTGGTCCGTTGGATGCATATTCGCTGAAATGGTGACTCAAAGGCCTCTGTTCCCTGGTGATTCAGAGATTGATGAGTTATTCAGAATATTCAGgtat--actctagaatcctg---gatattcacggagattcgc-taactgggaattggcaa-agtgcttgttaatatctcagtgtcaaccatatagctac-ctgatgaa-

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|33688520|gb|CF316759.1|CF316759
EST:     CCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAG                         TATTATGGGCACTCCAAATGAAGAAACTTGGCCAGGTGTTGCTTTACTACC
genomic: CCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattt ... gtcaatgaagTATTATGGGCACTCCAAATGAAGAAACTTGGCCAGGTGTTGCTTCACTACC
EST: gi|86427446|gb|CI072543.1|CI072543
EST:     CTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAG                         TATTATGGGCACTCCAAATGAAGAAACTTGGCCAGGTGTTGCTTCACTACC
genomic: CTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattt ... gtcaatgaagTATTATGGGCACTCCAAATGAAGAAACTTGGCCAGGTGTTGCTTCACTACC
EST: gi|88832780|gb|CI369670.1|CI369670
EST:     TAAGATTTTCAG                         TATTAT-GGCACTCCAAATGAAGAAACTTGGGCCAGGTGTTGCTTCACTAC
genomic: TAAGATTTTCAGgtcttaattt ... gtcaatgaagTATTATGGGCACTCCAAATGAAGAAACTT-GGCCAGGTGTTGCTTCACTAC
EST: gi|33678285|gb|CF306524.1|CF306524
EST:     CCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAG                         TATTATGGGCACTCCAAATGAAGAAACTTGGCCAGGTGTTGCTTCACTACC
genomic: CCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattt ... gtcaatgaagTATTATGGGCACTCCAAATGAAGAAACTTGGCCAGGTGTTGCTTCACTACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAATGGTGAATCAGAAGCCACTATTTCCTGGAGATTCTGAGATTGATGAACTCTTTAAGATTTTCAGgtcttaattttcaaatgttattaagtcttcatgttcttccatgtttctgaacaaagacaggaagacctaacactgctctatacattttcatgtgttcatgtcaatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT