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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCAAGGGTTACTAGGTATGTGTGTCGGTGAAAAGAGGAAGCTAAAGATACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctgaatatttgtttgtttgcttgatggtttcttgtgaaagaattatccatgtgtagattctcaactttgacatggctattttaccatgtttcacacctacattttacattgccaacagggcatgtgataagttttttcccatttacctataatactgacatacggtttcgtaaccaatag

Basic information

species Oryza sativa
transcript LOC_Os01g68710.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68710.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G153991_T01 (Zea mays), 5'ss of exon 5
GACCAAGGGTTACTAGGTATGTGTGTCGGTGAAAAGAGGAAGCTAAAGATACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctgaatatttgtttgtttgcttgatggtttct-tgtgaaagaattatccatgtgtagattctcaactttgacatggctattttaccatgtttcacacctacattttacattgccaacagggcatgtgataagttttttcccatttacctataatactgacatacggtttcgtaaccaatag
|||||||| || || |||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||||||| |||||||||||||||| ||||  |||||| || |||| || |||||||  |||||   ||| |  | |||  |   ||||  ||||  | | || ||||||||   |  |                                                                                        
GACCAAGGATTGCTCGGTATGTGCGTGGGTGAAAAGAGGAAGCTAAAGATACCTGCAAAGATGGGTTATGGTGAGCGAGGCTCCCCACCAAAGATTCCAGgtatgg-ctgatgatttgtctgcttgcatgctggtttccatgtgacgaaatgaatcctgtagattctctcttctttagcgtagccattttacctcatccct---------------------------------------------------------------------------------------

upper sequence: LOC_Os01g68710.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G031204_T01 (Zea mays), 5'ss of exon 5
GACCAAGGGTTACTAGGTATGTGTGTCGGTGAAAAGAGGAAGCTAAAGATACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctga--atatttgtttgtttgcttgatggtttcttgtgaaagaattatccatgtgtagattctcaac-tttgacatggctattttaccatgtttcacacctacattttacattgccaacagggcatgtgataagttttttcccatttacctataatactgacatacggtttcgtaaccaatag
|||||||| || ||||||||||| |||||||||||| |||||||||||||||||||||||||||| ||||| ||| ||||||||||||||||||||||||||||||   ||   | |||||||| ||||| | ||||| | ||||||  |||||| | |||  |   ||||    |    | ||||  ||| | |  ||                                                                                           
GACCAAGGATTGCTAGGTATGTGCGTCGGTGAAAAGCGGAAGCTAAAGATACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctagatggtttttgtttgcttgctcgctggttccatgtgaagaaattattcgtgtagattctctccgtgtccagcgtggccgtttcatctcgtc------------------------------------------------------------------------------------------
















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|29679614|gb|CB675889.1|CB675889
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|699803|gb|D46094.1|D46094
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|3762510|gb|AU029262.1|AU029262
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|88295466|gb|CI527829.1|CI527829
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|55413110|gb|CV725486.1|CV725486
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTAGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|55438455|gb|CV732524.1|CV732524
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCCCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|88420519|gb|CI562153.1|CI562153
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|88276548|gb|CI397350.1|CI397350
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|33659573|gb|CF282186.1|CF282186
EST:     GCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: GCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|88242499|gb|CI242348.1|CI242348
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|9055415|gb|AU097613.1|AU097613
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|88207641|gb|CI207490.1|CI207490
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|86824178|gb|CI260793.1|CI260793
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTGATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|86829393|gb|CI285036.1|CI285036
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGC-T-TCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|88460304|gb|CI529379.1|CI529379
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|55436956|gb|CV731667.1|CV731667
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|15008509|gb|AU222897.1|AU222897
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCNCCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
EST: gi|86824137|gb|CI260768.1|CI260768
EST:     ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAG                         GTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA
genomic: ACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctg ... taaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCAAGGGTTACTAGGTATGTGTGTCGGTGAAAAGAGGAAGCTAAAGATACCTGCAAAGATGGGTTATGGGGAGAGAGGCTCCCCACCGAAGATTCCAGgtatggtctgaatatttgtttgtttgcttgatggtttcttgtgaaagaattatccatgtgtagattctcaactttgacatggctattttaccatgtttcacacctacattttacattgccaacagggcatgtgataagttttttcccatttacctataatactgacatacggtttcgtaaccaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA