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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC

Basic information

species Oryza sativa
transcript LOC_Os01g60040.1
intron # 50
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 51
gtttgctatttcaatcctggaggtgt------ttaagctagtt---------ttggtgtt-tttaac---tgattggct--attatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
|||||  |  ||| || ||  || |       ||  ||| |||         | | |||| ||| ||    |||||  |  ||||   | ||||  | |||||||||||||||||||| || ||||||||||  || ||||| |||||||||||||| || || ||||| ||| | ||||||  ||||||||||||||| || |
gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttg--taatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
gtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactga-------ttggctattat--cgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
||| |  || ||| |  |||||| |||| |||| ||| |  |  ||||   |||       |||  | | ||  |||| || ||  |||||||||||||||||||| || ||||||||||| || || || |||||| | ||||| || || ||||| ||| | ||||| ||||||||||| ||||| || |
gttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgca-atgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
------------------------------------------gtttgctattt-caatcctggaggtgtttaagc-tagttt--tggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAAT---TGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
                                           |||||  |||  | | ||    | | ||  |  ||||    | | || ||| ||  |||||| |||    |||     |  ||||| |||||||||||||||| |||||||||||||| || ||  | ||  |  | || ||||| ||      |  |  |||| | |||||  | |||||||||    
gttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgac-aattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 53
-----------------------------------------gtttgctattt-caatcctggaggtgtttaagc-tagttt--tggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAAT---TGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
                                           ||||  |||  | | ||   || | ||  |  ||||    | | || ||| ||  |||||| |||    |||     |   |||| |||||||||||||||| |||||||||||||| || ||  | ||  |  | || ||||| ||      |  |  |||| | || ||  | |||||||||    
gttgagttaatttacttgtattaccacatgttcttaattgaacttgcattttgtatttctaccggcgattgggagtagtagaattgagtatttgacc-attggcaattgat-tttaacattttggcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCGAGTTTACCGATGCCAACCCCTCCACCGGCATCTTTAAATATATCTTCCCCTGATTTTGCACCTC---

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|58675157|gb|CK063844.1|CK063844
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58658439|gb|CK047119.1|CK047119
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCA
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCA
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCC

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: 65 (upstream exon), 71 (downstream exon)
Score: 13

GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
             tgtttttaa  TA-rich tract