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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGTACCGTCATAGTGATGCTGCCAGGATGAATCCTAGGGATTGCTGGTATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactcccttgctctccgttttttttttcttcaaccaaaactactgcaattattatatgtttagtgccactgcgaaacatgccgacactgtaagctacta...

Basic information

species Oryza sativa
transcript LOC_Os02g58440.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G041799_T01 (Zea mays), 5'ss of exon 2
TGAGTACCGTCATAGTGATGCTGCCAGGATGAATCCTAGGGATTGCTGGTATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactcccttgctctccgttttttttttcttcaaccaaa-actactgcaattattatatgtttagtgccactgcgaaacatgccgacactgtaagctacta---------------------
 |||||||||||||| |||||||| ||||||||||| ||||| ||||||||||||||| ||||||||||||| |||||||||||||| || ||||||||||| |  |||   ||     |    | |  |  |  |||| || | ||| || |||   | ||  ||  |||    || |||| |||  ||  |  || ||                      
CGAGTACCGTCATAGCGATGCTGCGAGGATGAATCCCAGGGACTGCTGGTATTGGTTCCATGGCAACTGCGCAAATCCTAAATGCTCCTTTAGGCACCCGgtgcgtcctccgtccatcctccgctctcttcaatgcaaacacaaatgccatgattgcttattacgtaacac----aagcatgacgatgcttcactctgcttctatcttcttttttcccccag
















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|88734924|gb|CI758432.1|CI758432
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGT
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGT
EST: gi|88353169|gb|CI654435.1|CI654435
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
EST: gi|88357818|gb|CI625069.1|CI625069
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
EST: gi|88735151|gb|CI758659.1|CI758659
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGT
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGT
EST: gi|29640554|gb|CB645563.1|CB645563
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
EST: gi|29627028|gb|CB632039.1|CB632039
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
EST: gi|88760981|gb|CI770537.1|CI770537
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
EST: gi|88742632|gb|CI766140.1|CI766140
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATC
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATC
EST: gi|88573922|gb|CI665691.1|CI665691
EST:     ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCG                         CCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA
genomic: ATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAA

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: 72 (upstream exon), 52 (downstream exon)
Score: 4

TGAGTACCGTCATAGTGATGCTGCCAGGATGAATCCTAGGGATTGCTGGTATTGGTTCAATGGCAACTGCGCTAATCCTAAATGCTCATTCAGGCACCCGgtactccctt ... cacttttcagCCGTTGGATGGCCTGGTCGGAGCACCCACAACACCACGAACATCTCAACAATCTGCACCACAGGTTTCTGTGCCTGCTCAAGCTCCTGTGCCTAATCCTG




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