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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCCTGGACAATGTGAAAGGATGCACTGATCAGGTGGAGAATGGAACCAAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgttttctttataagtcacatttcatttatggtatcatcagtgtgattacttcgatggaatcatagaagcactgaagatcaggatttaaacctc...

Basic information

species Oryza sativa
transcript LOC_Os03g21460.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21460.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G031825_T05 (Zea mays), 5'ss of exon 2
GATCCCTGGACAATGTGAAAGGATGCACTGATCAGGTGGAGAATGGAACCAAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgttttctttataagtcacatttcatttatggtatcatcagtgtgattacttcg---atggaatcatagaagcactgaag-atcaggatttaaacctc
|||||||||||||||||||||| |||||||||||||||||||||||||  || ||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||||| |  |||    |    ||  |||||  || | | |||   |   || |    |||| || ||   ||  |||| | ||      | |||    
GATCCCTGGACAATGTGAAAGGCTGCACTGATCAGGTGGAGAATGGAATGAAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtttgc--tatgctccttcctttctttattataacgtaagtcccacctctccatttatggtataatgtcagtgctgatgcataccagctcaaaga--
















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|33687222|gb|CF315461.1|CF315461
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGTCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|33687113|gb|CF315352.1|CF315352
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|33808256|gb|CF330017.1|CF330017
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACGCACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|33654738|gb|CF277352.1|CF277352
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|58593206|gb|CF991514.1|CF991514
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACT
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACT
EST: gi|218494169|gb|FG952751.1|FG952751
EST:     TACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: TACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|2443021|gb|C74792.1|C74792
EST:     AAATTGTCCCTTGGGAANGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|218495156|gb|FG966275.1|FG966275
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTA
EST: gi|66913473|gb|CX100321.1|CX100321
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|33659109|gb|CF281722.1|CF281722
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|88762168|gb|CI771724.1|CI771724
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
EST: gi|33661942|gb|CF292909.1|CF292909
EST:     AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTG                         CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA
genomic: AAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGA

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: 64 (upstream exon), 62 (downstream exon)
Score: 25

GATCCCTGGACAATGTGAAAGGATGCACTGATCAGGTGGAGAATGGAACCAAATTGTCCCTTGGGAAGGACATTGAGATACTATGCCTGCACACACCGTGgtatgctgtt ... cttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG




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