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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACCGTGCTGCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaagccatgcgccgatctgctcgcctccctccgctggtgtccccgtccatatgatccgatctgacgccgtgtttttttttctctcttccttgtctcccttttgggtctatgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os12g06020.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G39120.1 (Glycine max), 5'ss of exon 1
CCTCACCGTGCTGCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaagccatgcgccgatctgctcgcctccctccgctggtgtccccgtccatatgatccgatctgacgccgtgtttttttttctctcttccttgtctcccttttgggtctatgtgtgcag
 ||||| || || || ||  ||||||||  ||| || || || |||||||||||||| || |||||  ||||||| ||||||||||| ||||  || |||||         ||  | |        |  | | | || | |  | |   | |||        |  |||          | |  |  |||||||||  |  | | ||   |              
TCTCACTGTTCTCCAACGAATCGACCCCTTCGTTGAAGAAATTCTCATCACCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgt--------tcactctctttctatttttcttacttctgtttttattttcatcc--------cattct---------ctctcatcgctctcttccgcgattgctttgcag--------------

upper sequence: LOC_Os12g06020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G08370.1 (Arabidopsis thaliana), 5'ss of exon 1
CCTCACCGTGCTGCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaagccatgcgccgatctgctcgcctccctccgctggtgtccccgtccatatgatccgatctgacgccgtgtttttttttctctcttccttgtctcccttttgggtctatgtgtgcag
 ||||| || || |||||  |||| ||   | ||||||| ||||||||||| ||||| || |||||  |||| || |||||||| ||||||| ||| |||||  ||       |    | ||||  |||  | | |    || |||   | ||| ||      ||| |||  | || |||| |  |                                      
TCTCACAGTTCTCCAGCGGATCGATCCATACATCGAGGAAATCCTCATCACAGCCGCTCATGTCACTTTCTATGAATTCAACATTGAGCTCAGCCAATGGgttagt------ctcaatcaatct--tcgattacataatttgatgtttgcttccctacctaatgat-tgat-ctgtcttttgtcattcag----------------------------------
















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|29684686|gb|CB680961.1|CB680961
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|29676701|gb|CB672976.1|CB672976
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|33793549|gb|CF322657.1|CF322657
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|58686519|gb|CK075206.1|CK075206
EST:     TCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: TCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|29639082|gb|CB644091.1|CB644091
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|29669200|gb|CB665475.1|CB665475
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|33793116|gb|CF322439.1|CF322439
EST:     GTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: GTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|88727764|gb|CI749566.1|CI749566
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|88433452|gb|CI594266.1|CI594266
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|58685061|gb|CK073748.1|CK073748
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|58694565|gb|CK083252.1|CK083252
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|29639128|gb|CB644137.1|CB644137
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|58660010|gb|CK048690.1|CK048690
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|88357134|gb|CI616021.1|CI616021
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
EST: gi|87008879|gb|CI304822.1|CI304822
EST:     CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG
genomic: CCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG

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: 67 (upstream exon), 51 (downstream exon)
Score: 34

CCTCACCGTGCTGCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaag ... atgtgtgcagAGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCACCGTGCTGCAGCGCCTCGACCCCGCCGTCGAGGACATCCTCATCACCGCCGCCCACGTCACGCTCTACGACTTCAACATCGAGCTCAACCAGTGGgtgggtgaagccatgcgccgatctgctcgcctccctccgctggtgtccccgtccatatgatccgatctgacgccgtgtttttttttctctcttccttgtctcccttttgggtctatgtgtgcag

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