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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgac-cttgatcacatacatagtcctttgg-gttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
|||||||||||||||||||| |||||||||||||||||||||| |||||| ||||| |||||||||||  | ||||||||||| |||||||| || |||||||||   ||   ||||        |   | || |||  |      ||  |       || ||| || | | |  ||| |||    ||| | |    
AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttaca-taagtgtgattttgccttgatgcag--

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacatacatagtcctttgg-gttggtaacaactgcgatca-tctgtcttgcatatacttatcgtgctttgattttggt----acgcag
||||||||||||||||||||||||||||||||||||||||||| |||||| || || |||||||||||  | ||||||||||| |||||||| |||||||||||| |    ||    |   |  || ||||    |||||     |    |   |  ||  |   | | ||||      | ||||||| |     | ||||
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctc--atgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgt-tcgaccttgatcacatacat----agtcctttgggttg--gtaacaactgcgat-----catctgtcttgcatatacttatcgtgctttgattttggtacg-cag-----------
|||||||| ||||||||||||||||||||||| || ||||||||||||||||| || || ||||||||| | || || ||||| ||||| ||||||||||||  ||   |   | |  ||  |    | |   |||    |  || | || |   ||     ||  |   |||| ||  | || |    | | ||  | ||  | ||            
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccgtagtctgtaatgtagcttttaaattacttgtcccgaagtcataaatattatttacgcaattagattgc-taagcataacactttctaatcgttgtgtggcaatatctatccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacc-ttgatcacatacatagtcctt--tgggttggtaacaactgcgatcatctgt-cttgcatat----acttatcgtgctttgattttggtacgcag--------------
|||||||| ||||||||||||||||||||||| || ||||||||||||||||| || || ||||||||| | || || ||||| ||||| |||||||||||| | ||  |   | |  ||  |  || ||  | |    | ||        || || | | |  | | ||    ||  ||    ||||    ||| |  |  |              
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtactacagtctgtaatctaacttctcattacttgtccagaaatcctaaatattatttatgcaagtagattgccacgcattacactttctcattgttgtgtggctctctggatccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttc----gaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgt-cttgcatat----acttatcgtgctttgattttggtacgcag--------------
|||||||| ||||||||||||||||||||||| || ||||||||||||||||| || || ||||||||| | || || ||||| ||||| |||||||||||| |    | |  | |||  |    |       | |    | ||  |     || || | | |  | | ||    ||  ||   ||| |    ||| |  |  |              
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAGGAAACCAAAGgtactgtagtctgtaatctaacttctcaattacttgtccagaaatcataaatattatttatgcaagtagattgtgacacattacgctgtctcattgttgtgtggctctctggatccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
|||||||| |||||||| |||||||||||||| || ||||||||||||||||| || || ||||||||| | || || ||||| ||||| ||||||||||||   ||| |  ||   || ||| |  ||  ||  |   |   ||   | |||    |||   | || || | |||     || |   ||  |||
AAGGAGCCAAACAAGGGGGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgt---accatagtc-tgtaaatattatttatggaagtagattgcta--agcattacactt---tctaattgttgtgtggcaatctc--tatccag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacata-catagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
||||| |||||||||||||| ||||| |||||||||||||||| ||||||||| || || ||||||||| | || || ||||| ||||| || |||||||||   |  |  ||    || ||  | ||  | | | | |    |  | |      ||  | | | | | ||    || | |  || |   | ||||
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatat--ttgttccatgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
|| || |||||||||||||| ||||| ||||| || ||||| ||||||||||| || || ||||||||  | || || ||||| ||||| ||||||||||||   |  |  ||| |  ||    | |   |       ||   |   | |     || ||||  |  ||| |  ||  ||| ||   |||  |||
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttccatc-ctcaccatcttcgcagaaccttcaatggc-atggttgaaagt-ttgctaactcttgttctg--ttgtttcatgtat-cag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EDP06859 (Chlamydomonas reinhardtii), 5'ss of exon 5
------------------AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCG-GTGACGAAACCAAAGgttcgacct-----tgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
                  |||||||||||||||||||||||||| |||||||| || ||||| || || || || |||||    || |||||||| || || | |||      | |  || |           ||  |   |  || |   |||  | | |     |  |||  | |  ||   |||  | |  |  | |                   
CGCGAGTGGTTCGGCGGCAAGGAGCCCAACAAGGGTGTCAACCCCGATGAGGCCGTGGCCTACGGCGCGGCCGTGCAGGGCGCAATCCTCAGCGGGGAAGgtgcgtgggagggcgagtggataagtggatggatggacgggtggatgggagtttctggtaggtgggagggcgtgcgtgcgtgaggcaggtgcacaaaggg-------------------

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
|||||||| ||||||||||| ||||| || |||||||| || | ||||||||| || |||||  | ||  | ||||| || ||||| |||||    |||||        | | || |||| |      ||  ||   |  || ||| |     ||  |  || |  | | |  |                     
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGg--------taagcaaatacttgtcttcttttgtaatt--catctgtg-----ctaacgcgcgtccattgacag---------------------

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcg----accttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag
|||||||| ||||||||||| ||||| || |||||||| || | ||||||||| || |||||  | ||  | ||||| || ||||| |||||    ||||||  |      ||||    | |   || ||| |  |  || ||||    |||  ||||                                         
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctg--tgctaacg--cgcgtccatcgacag------------------------------------

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|2310214|gb|C26369.1|C26369
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTNACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCNTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
EST: gi|29655799|gb|CB652074.1|CB652074
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
EST: gi|29640637|gb|CB645646.1|CB645646
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
EST: gi|58690929|gb|CK079616.1|CK079616
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
EST: gi|2310033|gb|C26188.1|C26188
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGT
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGT
EST: gi|58661511|gb|CK050191.1|CK050191
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
EST: gi|55411112|gb|CV723488.1|CV723488
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
EST: gi|29660696|gb|CB656971.1|CB656971
EST:     TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG
genomic: TGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCG

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: 75 (upstream exon), 74 (downstream exon)
Score: 194

AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgacctt ... tggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCGGTGGAGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAA




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