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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactcagctccctcctcaacatgtacccacacaggcagtaccagtatgataactcccttcctcgaaaagaaagtatgataattctctaaggcttccttttctttcgttacaccatgtggcag

Basic information

species Oryza sativa
transcript LOC_Os01g69900.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69900.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G438077_T01 (Zea mays), 5'ss of exon 9
AAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactcagctccctcctcaacatgtacccacacaggcagtaccagtatgataactcccttcctcgaaaagaaagtatgataattctctaaggcttccttttctttcgttacaccatgtggcag
||| |||||||||||||||  ||||||| |||||||| |||||| | ||||||||||| || |||||| |||| |||||||||| |||    |||   || |   || ||| |    ||   |   || || |  | | | || || |     |     |||    |  ||| | |     | |   | | |||||      |||     |||
AAATGAGCAGCTTGACAGACCTGATAACTAGCATTCTTCAGAGGGTCGGCGATGACATTGACAGAAAACACCTGCCACAAATTTCGgt----actggactactggctgaacctagtgcctttc--tcaatatc--tgtaacaattcacacgaccatttcgaa---ttcctaagtttaatttgttctttgtcctttcccggtgccactctacag

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G059310_T01 (Zea mays), 5'ss of exon 1
--------------AAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactcagctccctcctcaacatgtacccacacaggcagtaccagtatgataactcccttcctcgaaaagaaagtatgataattctctaaggcttccttttctttcgttacaccatgtggcag
              |||||||||||||||||||  | ||||| |||||||| |||||| | || |||||||| || |||||| || | ||||||||||||||    |||   || |   || ||| |    ||   |   || || | |||  |   | | |  ||     ||     || | | | | | |      |||||| |    |  || | |        
GTTGGGAATGTCAGAAACGAGCAGCTTGACAGACCTAATAACTAGCATTCTTCAGAGGGTCGGAGATGACATTGACAGAAAACACATGCCACAAATTTTGgt----actggactactggctgaacctagtgcctttc--tcaatatctgtaacaattcacacggccatttcaaattcctacgtttaatttattctttgtcctttcccggtgccactctacaa-----

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G133621_T01 (Zea mays), 5'ss of exon 9
AAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactcagctccctcctcaacatgtacccacacaggcagtaccagtatgataactcccttcctcgaaaagaaagtatgataattctctaaggcttccttttctttcgttacaccatgtggcag
|||||||||||||||||||  ||||||| |||||||| |||||| | ||||||||||| || |||||| |||| ||||||||||||||    |||   || |   || ||| |    ||   |   || || | |||  |  | || |     |     |||    |  ||| | |     | |   | | |||||      |||     |||
AAACGAGCAGCTTGACAGACCTGATAACTAGCATTCTTCAGAGGGTCGGCGATGACATTGACAGAAAACACCTGCCACAAATTTTGgt----actggactactggctgaacctagtgcctttc--tcaatatctgtaacaatattcacacggccatttcgaa---ttcctaagtttaatttgttctttgtcctttcccggtgccactctacag

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G171622_T01 (Zea mays), 5'ss of exon 12
AAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactcagctccctcctcaacatgtacccacac-aggcagtaccagtatgataactcccttcctcgaaaagaaagtatgataattctctaaggcttccttttctttcgttacaccatgtggcag
|||| ||| || || ||||| |||||||||||||||| |||||| | ||||| ||||| || |||||| |||| || ||||||||||||  | || | |     |    || |    | |||| || ||||||| |  |    | | |  |   | ||          |   |||||||    ||| |        |  |||||          
AAACAAGCGGCCTGGCAGAGCTGATAACCAGCATTCTTCAGAGGGTCGGCGACGACATTGACAGAAAACACCTGCCGCAAATTTTGgtactggctgaac-----ctaacaccttcgtcaacacgagacagtacccgcgttgctatttcgatttcctaa----------gtccattctctgtt-ctttcccggtgcccactacacag--------

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|88961167|gb|CI096571.1|CI096571
EST:     GATGACATCGATAGAAAAAACCTACCACAAATTTTG                         TATGAAGATGAGGATCATGATAAGGTCATACTTTTATCGGACAGTGACCTT
genomic: GATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
EST: gi|29626336|gb|CB631347.1|CB631347
EST:     TACAGAGGCTTGGCGATGACATTGATAGAAAAAACCTACCACAAATTTTG                         TATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
genomic: TACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
EST: gi|58692956|gb|CK081643.1|CK081643
EST:     TACAGAGGCTTGGCGATGACATTGATAGAAAAAACCTACCACAAATTTTG                         TATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
genomic: TACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
EST: gi|29660359|gb|CB656634.1|CB656634
EST:     TACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTG                         TATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
genomic: TACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
EST: gi|86433216|gb|CI093559.1|CI093559
EST:     CACAAATTTTG                         TATGGAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
genomic: CACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
EST: gi|29668009|gb|CB664284.1|CB664284
EST:     TACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTG                         TATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT
genomic: TACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTT

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: 63 (upstream exon), 74 (downstream exon)
Score: 32

AAACGAGCAGCTTGACAGAGTTGATAACCAGCATTCTACAGAGGCTTGGCGATGACATCGATAGAAAAAACCTACCACAAATTTTGgtaaggactc ... catgtggcagTATGAAGATGAGGATCATGATAAGGTCATACTTTCATCGGACAGTGACCTTGTAGCTGCTGTGGACCATGCAAGGCAAATCGGTTGGAAG




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