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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGTACATTTCGCACAAGTGGCCCTTCTGGAATAGAACAGATGGAGCAGACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgctaattcccttggcatctcacatttggatttgtctgtgtgtaattctctttctgatttcattgtttactttggagtttggacatacccttttagatgtcaacgctaaggataaaacattattttgaccttttctactcacaagttctgaagtagtgttattaactgttgtatactatttgtag

Basic information

species Oryza sativa
transcript LOC_Os04g32670.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32670.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G023020_T01 (Zea mays), 5'ss of exon 2
CCAGTACATTTCGCACAAGTGGCCCTTCTGGAATAGAACAGATGGAGCAGACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgctaattcccttggcatctcacatttggatttgtctgtgtgtaattctctttctgatttcattgtttactttggagtt-tggacatacccttttagatgtcaacgctaaggataaaacattattttgaccttttctactcacaagttctgaagtagtgttattaactgttgtatactatttgtag
||| || |||||  |||| ||||||||||||||||| || ||||||||||| || ||||| ||||| |||||||||||||  ||||| || |||||||||||| |    |     |||  |||      |   |  ||| ||   | |||| |  |     |  | |   ||||||    |||| |     || |  ||     | ||   | |                                                                             
CCAATATATTTCAAACAAATGGCCCTTCTGGAATAGGACTGATGGAGCAGATCATTTCTTCGTTGTTCCGCATGATTTTGCAGCATGCTTCCACTATCAGgtgaggttcaccatgcttttcatt--gtgtgcagtcttgcct---tttaatgcctt-----aacttacattttactcacaagttgtatgtgtaacgattgtatcggcatttccag----------------------------------------------------------------------------

upper sequence: LOC_Os04g32670.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 5'ss of exon 2
CCAGTACATTTCGCACAAGTGGCCCTTCTGGAATAGAACAGATGGAGCAGACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgctaattcccttggcatctcacatttggatttgtctgtgtgtaattctctttctgatttcattgtttactttggagtttggacatacccttttagatgtcaacgctaaggataaaacattattttgaccttttctactcacaagttctgaagtagtgttattaactgttgtatactatttgtag
 |||   ||| |   ||| ||||| | ||||||| | ||||| ||||||||||||||||||||||| || ||||| ||||| || ||||| || ||||| ||      ||    | ||    |||||   |    ||| ||| | |   || ||   |  | |||  ||| ||  |    | ||     | ||  || || |||     |                                                                                
TCAGCTTATTGCTTCCAATTGGCCATACTGGAATCGCACAGAAGGAGCAGACCACTTCTTTGTTGTGCCTCATGACTTTGGAGCCTGTTTCCATTATCAAgtaaacaatagaatcttt----tctcagtctc---tttttctttct---atcctaagtaggctttgcttgcttgatcaatacttc---tacactattctaaatgatggtgtgc-----------------------------------------------------------------------------
















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|27577458|gb|CB000153.1|CB000153
EST:     ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAG                         GAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCTACGTGCTACG
genomic: ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgcta ... ctatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
EST: gi|702132|gb|D48423.1|D48423
EST:     ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAG                         GAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
genomic: ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgcta ... ctatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
EST: gi|29656014|gb|CB652289.1|CB652289
EST:     ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAG                         GAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
genomic: ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgcta ... ctatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
EST: gi|25797157|gb|CA753118.1|CA753118
EST:     ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAG                         GAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
genomic: ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgcta ... ctatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
EST: gi|86847895|gb|CI288898.1|CI288898
EST:     ACCACTTCTATGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAG                         GAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG
genomic: ACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgcta ... ctatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 39

CCAGTACATTTCGCACAAGTGGCCCTTCTGGAATAGAACAGATGGAGCAGACCACTTCTTTGTTGTCCCGCATGATTTTGGTGCATGTTTTCACTATCAGgtgtgtgcta ... ctatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACGTTGGTCCAAACATTTGGACAGGAGAACCATGTTTGCTTAAAAGAGGGTT




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