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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccag

Basic information

species Oryza sativa
transcript LOC_Os01g16900.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 3
TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccag
|||||||||||||||||| ||||||||  |||| |||||||| |||||||| || |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||| |  || |   ||  |||  | |    |  ||| ||  ||||  |||  || ||   || |||
TTGCAACAGCCTCCCAGGTTACAAGACCAGATACGATGATGTTAACCTTGTAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaa-gagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcag

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 3
TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttcattggt-----cttgttagcattattcat---cactgtgtgctatttattctccag
|||||||||||||||||| ||||||||  |||| |||||||| ||||||||||| |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||| |  || |   ||  |||  |      |||| ||||| |||| |   |||  ||| ||| ||   ||||||
TTGCAACAGCCTCCCAGGCTACAAGACCAGATACGATGATGTTAACCTTGTGACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattcttaaa-gagatgttgcttcaattattgtcagtttgtcagcatgattctttttcaccctgtcctagtttcgctccag

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G06590.2 (Glycine max), 5'ss of exon 2
TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttc-attggtcttgttagcattattcatcactgtgtgctatttatt--ctccag
|||| |||| || ||||| ||||| |||||||||||| |||| || ||  | || |||||||||||||| || || || || ||||| ||||| ||||||||||   |    | ||   || | |  | | ||   | |  ||   || | |      ||| |   ||||||      |||
TTGCTACAGTCTTCCAGGCTACAAAACTCGATATGATAATGTCAATCTAATTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgggtctcag

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|163928585|gb|EG710882.1|EG710882
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|14571344|gb|BI118712.1|BI118712
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|29639681|gb|CB644690.1|CB644690
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58593071|gb|CF991379.1|CF991379
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|29664534|gb|CB660809.1|CB660809
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58669476|gb|CK058162.1|CK058162
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|29619530|gb|CB624542.1|CB624542
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58691994|gb|CK080681.1|CK080681
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|66923182|gb|CX110030.1|CX110030
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccag

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