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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag

Basic information

species Oryza sativa
transcript LOC_Os03g01750.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01750.7 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G052546_T05 (Zea mays), 5'ss of exon 1
GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag
|||||||||||||||  ||||||| ||||||||| | ||||| ||  |||||  ||  || ||| | |||||||| ||||| ||||| ||||| || |||||||| | | |||   | |   |  |   ||   |  | |  | |  || |  ||   |     ||    ||||   |||||
GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagat-cctcctgtcccgtcaaatggatg---ccatagctgag--ggctgagagtgcacgcgtt--tttcttggctgcag
















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|58688312|gb|CK076999.1|CK076999
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCA
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCA
EST: gi|2428616|gb|C73079.1|C73079
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATACCTACGTCCAG                         GTCTCCAGGGATGGTACCANCGATGAAGAGNGAGA-TTAAGGGN-CGTTT-
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|38480383|gb|CF964472.1|CF964472
EST:     GCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGTGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: GCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88998256|gb|CI038141.1|CI038141
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88311093|gb|CI658006.1|CI658006
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|86900027|gb|CI300120.1|CI300120
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|58690530|gb|CK079217.1|CK079217
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT