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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCCTTCTAGTAGGAAAGAAGTGATTGAGCTTCTCGATATACTATTAAGGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaatcactatgctggttattctgtgccttattttctttttctctgggctatcacttattcgatttctgtgtatcttctgtgctgtttttacctttag

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 35
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 35
lower sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 17
ATTGCCTTCTAGTAGGAAAGAAGTGATTGAGCTTCTCGATATACTATTAAGGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaat---cactatgctggtta----ttctgt--gccttattttctttttctctgg-gctatcactta-ttcgatttctgtgtatcttctgtgctgtttttacctttag
| | | ||| ||| ||||||||| |||||| ||||| || ||||||||||||||| ||||||| || ||||||||||||||||||||||||||| ||||||| |||    |  |  || ||||    |  |||  || |||||| |||||  |   |  | || || || || |||| ||||      | ||| ||  ||| || | |||
ACTTCTTTCGAGTGGGAAAGAAGCGATTGAACTTCTTGACATACTATTAAGGTGGATTGTCTTACGCTTTTGTGAATCTAACACAACATGTTTGTTGAAGgtgaatgcatagcactcttgttaagaatcatgttggcattatttccttttattgcagcacaataacctaatttgattcctgtac----tgtgtactactttcacttctag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 35
lower sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 33
ATTGCCTTCTAGTAGGAAAGAAGTGATTGAGCTTCTCGATATACTATTAAGGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaat---cactatgctggtta----ttctgt--gccttattttctttttct-ctgggctatcacttattcgatttctgtgtatcttctgtgctgtttttacctttag
| | ||||| ||| |||||||||||||||| ||||| || ||| ||||||||||||||||||| || ||||||||||| ||||||||||||||| ||||||| |||    |  |  || ||||    |   ||  |||||||||  ||||  | |||  | || || || |   |||||   |    | ||| ||  ||| |  |  ||
ACTTCCTTCAAGTTGGAAAGAAGTGATTGAACTTCTTGACATATTATTAAGGTGGTTTGTCTTACGCTTTTGTGAATCGAACACAACATGTTTGTTGAAGgtgaatgcataacactcttgttaagaatcacgttggccttatttctttttgttgctgcacaataacctaatttgtttct---tgcactgtgtactactttgatttacag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 35
lower sequence: GRMZM2G014635_T01 (Zea mays), 5'ss of exon 1
---ATTGCCTTCTAGTAGGAAAGAAGTGATTGAGCTTCTCGATATACTATTAAGGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaat--------cactatgctggttattctgt--gccttattttctttttctctgggctatca--cttattcgatttctgtgtatcttctgtgctgtttttacctttag
   | | ||||| ||| |||||||||  ||||| ||||| || ||||||||||||||| ||||||| || ||||||||||||||||   |||||||| ||||||| |||        | || || |    ||  |||  || |||||| |||||  |   |  ||  |  || ||| |||| ||||      | ||| ||  ||| || | |||
GGCACTTCCTTCGAGTGGGAAAGAAGCAATTGAACTTCTTGACATACTATTAAGGTGGATTGTCTTACGCTTTTGTGAATCTAACA---CATGTTTGTTGAAGgtgaatgcataacactctttgttaagaatcatgttggcattatttccttttattgcagcataataacctaatttgattcctgtac----tgtgtactactttcacttctag

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|88665316|gb|CI711114.1|CI711114
EST:     GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAG                         GTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
genomic: GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaatcact ... ttacctttagGTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
EST: gi|88664232|gb|CI673700.1|CI673700
EST:     GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAG                         GTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
genomic: GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaatcact ... ttacctttagGTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
EST: gi|88592754|gb|CI710878.1|CI710878
EST:     GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAG                         GTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
genomic: GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaatcact ... ttacctttagGTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
EST: gi|396941288|gb|HO188497.1|HO188497
EST:     GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAG                         GTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC
genomic: GGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaatcact ... ttacctttagGTGCTTGACTTCCTTCCTGAGCTCTTTGATGTTCTGAAAGATCAGTCATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCCTTCTAGTAGGAAAGAAGTGATTGAGCTTCTCGATATACTATTAAGGTGGTTTGTCTTGCGATTTTGTGAATCTAACACAACATGTTTGCTGAAGgtaaatcactatgctggttattctgtgccttattttctttttctctgggctatcacttattcgatttctgtgtatcttctgtgctgtttttacctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG