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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCACTCATCAGACTTCATGCTGATTACCTTCTTGTTGTTGGAGTTTGCTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagacttctcttgaagagaattccgtgtttctcgttagaaaagtctacatggcatgtaagatgcaattctgttagaggattttttttttttggtgt...

Basic information

species Oryza sativa
transcript LOC_Os01g22870.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g22870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G800558_T01 (Zea mays), 5'ss of exon 1
TTCTCACTCATCAGACTTCATGCTGATTACCTTCTTGTTGTTGGAGTTTGCTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagacttctcttgaagagaattccgtgtttctcgttagaaaagtctacatggcatgtaag--atgcaattctgttagaggattttttttttttggtgt
||||| |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||| ||| |||| |||||||| ||||| |||||||      ||||| || |  | || |  || | |    | |||||   ||      ||| |||  | |||    | ||   | |  || |   |  |   |
TTCTCGCTCATCAGACTTCAAGCTGATTACCTTCTCGTTGTTGGAGTTTGCTTGAGCCTCAGCATTGCAAATATTATTGGGTTCACCAAATGCAATAAAGgtgcaca--ttctcctgtattgcatccaatgctaccttgttgaaaaacttatgattgatgaaagtaaagcatgcatatttttgaagcttatcaatcagtcat

upper sequence: LOC_Os01g22870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G28620.1 (Glycine max), 5'ss of exon 5
TTCTCACTCATCAGACTTCATGCTGATTACCTTCTTGTTGTTGGAGTTTGCTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagacttctcttgaagagaattccgtgtttctcgttagaaaagtcta-----catggcat-gtaagatgcaattctgttagaggattttttttttttggtgt
||||||||||| || ||||| |||||||| || |||||||| ||||| ||  |||  |||||||| ||||| |||||||| || ||||| ||||| |||||| ||  | || | ||||  | | |       |    |||    || ||       | |   || | || ||    ||  ||| ||||| || | |   |      
TTCTCACTCATAAGGCTTCAAGCTGATTATCTCCTTGTTGTAGGAGTGTGTCTGACCCTCAGCATTGCAAATATTGTTGGTTTTACCAAATGCAAAAAAGgtcagtaagtt-tattgataatattcttaaaatgtatgtttcccaattcccactctcctaatatagcaaaattgttttaggttggaggaattgtctgcata-----

upper sequence: LOC_Os01g22870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G22720.1 (Glycine max), 5'ss of exon 5
TTCTCACTCATCAGACTTCATGCTGATTACCTTCTTGTTGTTGGAGTTTGCTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagacttctcttgaagagaattccgtgtttctcgttagaaaagtctacatggcatgtaagatgcaattctgttagaggattttttttttt-tggtgt-
||||||||||| || ||||| |||||||| || |||||||| ||||||||  |||  || ||||| ||||| |||||||| || ||||| ||||| |||||| ||  | || | ||||  | | |       |    |||    |       |    | | || ||    ||  ||| ||||| || | |   | | ||   
TTCTCACTCATAAGGCTTCAAGCTGATTATCTCCTTGTTGTAGGAGTTTGTCTGACCCTTAGCATTGCAAATATTGTTGGTTTTACCAAATGCAAAAAAGgtcagtaagtt-tattgataatattcttaaaatgtgtgtttctcactctcctaatata-gcaaaattggtttaggttggaggaattgtctgcatatagtaag

upper sequence: LOC_Os01g22870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv07s0005g01960.t01 (Vitis vinifera), 5'ss of exon 5
TTCTCACTCATCAGACTTCATGCTGATTACCTTCTTGTTGTTGGAGTTTGCTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagacttc--tcttgaagagaattccgtgtttctcgttagaaaagtctacatggcatgta-agatgcaattctgttagaggattttttttttttggtgt-
|| ||| |||| ||| || |  |||| ||  | || ||||| || ||||| ||||| |||||||| |||||||||||||| ||||| |  ||   |||||||  |   || |  |  |   ||   || | | | | | ||   |  |    | || |  |||  ||| |  |||   |||  |   ||   |      |  | 
TTTTCAATCATAAGATTTGAACCTGACTATGTCCTAGTTGTGGGCGTTTGTTTGAGCCTCAGCATTGCAAACATTGTTGGATTCACTAGATGTCGCAAAGgtatgcagctacatttctttcgaccctttcctatatttagtagcagta--taatattgtttgtttagaggtgattt--ttaatgctcttacatacccatgctta

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|88319599|gb|CI518443.1|CI518443
EST:     AGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: AGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|58684863|gb|CK073550.1|CK073550
EST:     CTTGAGTCTCAGCATAGCCAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|33680657|gb|CF308896.1|CF308896
EST:     CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|29678098|gb|CB674373.1|CB674373
EST:     CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|33680658|gb|CF308897.1|CF308897
EST:     CTTGAGTCTCAGCATAGCAAACAATGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|44679016|gb|CR292450.1|CR292450
EST:     CTTGAGTCTCAGCATAGCAAACATTGTTGGGTTCACCAAGTGCAACAAAG                         ATGTCAAGAAAAAAGTTGCAGATTGGACTAG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAG
EST: gi|29678099|gb|CB674374.1|CB674374
EST:     CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|27920913|gb|CB096721.1|CB096721
EST:     CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|86887714|gb|CI311847.1|CI311847
EST:     CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
EST: gi|218478253|gb|FG951116.1|FG951116
EST:     TTGAGTCTCAGCATAGCAAACAATTGTAGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCC
genomic: TTGAGTCTCAGCATAGCAAACA-TTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCC
EST: gi|86419153|gb|CI053954.1|CI053954
EST:     CTTGAGTCTCAGCATAGCCAAC-TTGTTGGCTTCACCAAGTGCAACAAAG                         ATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG
genomic: CTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTG

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), 71 (downstream exon)
Score: 25

TTCTCACTCATCAGACTTCATGCTGATTACCTTCTTGTTGTTGGAGTTTGCTTGAGTCTCAGCATAGCAAACATTGTTGGCTTCACCAAGTGCAACAAAGgtgagagact ... tatttttcagATGCCAAGAAAAACGTTGCAGATTGGACTAGAACTACGCTCCTATCATCTGGTGTCAGGTCAACAATTCAGTCAGCATTCGGTGTCTAAATAGAGGCGCC




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