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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTTCTACAATCTGGAGAAGTCCATATATTTGGGTATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaagatacatattagcaccaacatttaccataaaataatttaagaatttcatgtaaaaataaattgggatgttctgtatgaggaagtagtttctctgtttttaagtctgatgatatactagtgcctaaatagcattctcctgttatcgcag

Basic information

species Oryza sativa
transcript LOC_Os02g38840.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 3
GGATTTCTACAATCTGGAGAAGTCCATATATTTGGGTATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaagatacat-----attagcaccaacatttac-cataaaataatt-------taagaatttcatgtaaaaataaattgggatgttctgtatgaggaagtagtttctctgtttttaagtctgatgatatactagtgcctaaatagcattctcctgttatcgcag
|||||||| ||||||||||||||||||||||||||||| |||||||||||| |||| |||||||||||||||||||||||||||||||||||   ||         ||| | || |  ||| |   | | |||  ||       ||  |  | |   |     | || |   || ||   || || | |  || |||  || || |   |||      ||   | |   ||||| |  |  | |||         
GGATTTCTGCAATCTGGAGAAGTCCATATATTTGGGTACGCAAGATCAAATCTTTCTGATGATGGATTAAGAGAACGCATTCGTGGgtaagatctattttccttgaattggtacaagaattcatgtacagaatcgttacctctgtataatgtgccccttcctgttaactcatatttttgatacgatggaa-agattccatgattctttctct------atttgaatatataaatggtctattgctgcag------
















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|25798694|gb|CA754655.1|CA754655
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCACAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
EST: gi|88304205|gb|CI599893.1|CI599893
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATAC-TCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
EST: gi|29635730|gb|CB640739.1|CB640739
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
EST: gi|88443530|gb|CI596997.1|CI596997
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCAAAGGAGCTTCAGATGAACATA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATA
EST: gi|29616736|gb|CB621748.1|CB621748
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
EST: gi|88395088|gb|CI609404.1|CI609404
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAANGCATTCGTGG                         ATACCTCAAAGGAGCTTCAGATGAACATA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATA
EST: gi|88403178|gb|CI570919.1|CI570919
EST:     TATGCA-GATCAA-TATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCAAAGGAGCTTCAGATGAAC
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAAC
EST: gi|88445341|gb|CI587235.1|CI587235
EST:     TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCA-TTA
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATATTTCACAATTTTTGCAATTA
EST: gi|88345041|gb|CI625887.1|CI625887
EST:     TATGCCAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGG                         ATACCTCAAAGGAGCTTCACATGAACATATTTCAC
genomic: TATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaaga ... gttatcgcagATACCTCAAAGGAGCTTCAGATGAACATATTTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATTTCTACAATCTGGAGAAGTCCATATATTTGGGTATGCAAGATCAAATATTTCGGATGATGGATTAAGAGAACGCATTCGTGGgtaagaaagatacatattagcaccaacatttaccataaaataatttaagaatttcatgtaaaaataaattgggatgttctgtatgaggaagtagtttctctgtttttaagtctgatgatatactagtgcctaaatagcattctcctgttatcgcag

- - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA