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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca...

Basic information

species Oryza sativa
transcript LOC_Os02g51500.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51500.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G025470_T02 (Zea mays), 5'ss of exon 2
---CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca
   ||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||     | |||| |||| ||  ||||  ||||| |  |||      | ||   |||| | |  | | |      |      ||  
AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgccgacaatttcag--ccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgttt-

upper sequence: LOC_Os02g51500.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G025470_T01 (Zea mays), 5'ss of exon 2
CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca--
||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||     | |||| |||| ||  ||||  ||||| |  |||      | ||   |||| | |  | | |      |      ||    
CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAGTGgtattgccgacaatttcag--ccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgtttgtg

upper sequence: LOC_Os02g51500.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G012269_T01 (Zea mays), 5'ss of exon 2
CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca--
||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||    |||||  |  || |   ||||  ||| | |  |||      | ||   ||||   |  | | |      |      ||    
CGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGGTCCCAGGAGGTGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAGTGgtattgccgacaatttcagctctttgat--catagcattttcttggttcccatgacaaataacttgagttctatttccatatatttaattgaagtgtttgtc

upper sequence: LOC_Os02g51500.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G012269_T02 (Zea mays), 5'ss of exon 2
---CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca--
   ||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||    |||||  |  || |   ||||  ||| | |  |||      | ||   ||||   |  | | |    |  ||| || |    
AATCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGGTCCCAGGAGGTGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACAgtggtattgccgacaatttcagctctttgat--catagcattttcttggttcccatgacaaataacttgagttctatttccatata---tttaattgaagtgttt

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|58604515|gb|CK015043.1|CK015043
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAAGCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCC
EST: gi|29670191|gb|CB666466.1|CB666466
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|38475588|gb|CF959721.1|CF959721
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCC
EST: gi|88240110|gb|CI239272.1|CI239272
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88732429|gb|CI755606.1|CI755606
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGAT
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGAT
EST: gi|25799893|gb|CA755854.1|CA755854
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88436056|gb|CI516592.1|CI516592
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|33681776|gb|CF310015.1|CF310015
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88289982|gb|CI547619.1|CI547619
EST:     CATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: CATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|33684024|gb|CF312263.1|CF312263
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGGTGTACCATA
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGG-TGTACCATA
EST: gi|218499796|gb|FG963827.1|FG963827
EST:     AATTACGATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTG                         AGAAGCAGCTTGCGA
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGA
EST: gi|33683196|gb|CF311435.1|CF311435
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGNTGGGTGTACCATA
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATG-TGGGTGTACCATA
EST: gi|88478522|gb|CI415793.1|CI415793
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88471386|gb|CI408657.1|CI408657
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88511850|gb|CI439356.1|CI439356
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88481575|gb|CI418846.1|CI418846
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|88963349|gb|CI028365.1|CI028365
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
EST: gi|86853635|gb|CI330486.1|CI330486
EST:     AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACA---                         AGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC
genomic: AATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgc ... tcctttccagAGAAGCAGCTTGCGAATTCCCCCAAGCAGAACAGATGTGGGTGTACCATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca

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