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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G003509_T01 (Zea mays), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaa--------aactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag
||| |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||||||| | |||||||| ||||||||||||||||| ||||| | ||| |   | |         |  |||  |  |||   || |  |      |   ||| |  | |   | |  | |    ||| |      |||||||||
TCTACTCGCTATTGCTGAGGAGACATTGGCGGAGTTCATGTCCAAGGCGACCGGAACTGCTGTCAACTGGGTGCAGATGGTTGGGATGAAGgtgatgtacttgttttcttacatcgtgtagtacttgtatacaatgc-aatatcgtggcgaaaactatgctgatatctctgacctgattccaaacgcggtgctgattacag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag
||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||| | |||||||||||||||||||||||||||||||| | ||| | | ||| |   |||   ||   | || |  |  | |   | |||||  | |   ||  | |   | ||| |  |   ||||| |||
TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtacttgtttttctagata---gtgtgctaccctaatatggtgatgcacctgatgttgatatc--tctgaccgtttcaaacgtgatactgattgcag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G003509_T02 (Zea mays), 5'ss of exon 3
---------TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaa--------aactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag
         ||| |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||||||| | |||||||| ||||||||||||||||| ||||| | ||| |   | |         |  |||  |  |||   || |  |      |   ||| |  | |   | |  | |    ||| |      |||||||||
GTTTCCCAGTCTACTCGCTATTGCTGAGGAGACATTGGCGGAGTTCATGTCCAAGGCGACCGGAACTGCTGTCAACTGGGTGCAGATGGTTGGGATGAAGgtgatgtacttgttttcttacatcgtgtagtacttgtatacaatgc-aatatcgtggcgaaaactatgctgatatctctgacctgattccaaacgcggtgctgattacag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G13110.1 (Glycine max), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgta--atgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag
|||||| || |||||| |||||||| |||| | |||| | || || || || |||||||||||| | ||||| |||||| |||||||||||||   |  |||||  |            ||  || |   |  ||      | |  |||  | |  || |  ||    ||   |    |     || |  ||   
TCTTCTTGCAATTGCTCAGGAGACCCTGGCGGCGTTCCTTTCAAAAGCTACTGGAACTGCTGTCAACTGGGTCCAAATGATTGGGATGAAGgtgtgacctattcaataattcttcttcatggtcattgcttgcataaaacatatgtatttgtatgattatattttgcctctcattttttctgtcttcgtgtag--

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G13640.1 (Glycine max), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag--
||||||||| || |||||||||||| ||||||||||| | || ||||| || |||||||||||||| ||||| || ||| ||||||||||||||     ||  |  ||     ||    |   || |||   | |  |   |  |||  || | || |||||         |  | ||  | ||| | |      
TCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtatgccctttttaatattcttaattgcttgtgtttgtatgtatatttcataaatttgtgatattgttgttgtgtgtttgttcattgtgattttcaatgagtag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G02750.1 (Glycine max), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag---------------------
||||||||| || |||||||||||| ||||||||||| | || ||||| || |||||||||||||| ||||| || ||| |||||||||||||||||    ||||  | |    | || ||  |  || |  ||||   ||   ||   ||| |  ||  |  | ||    | |  |     | |  ||                         
TCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtaatgc-cccgtttaata----atctttgatgcttggttttttttctttcttatgtttgtataattcataaatatttgttaatgttgttgtgtttttgttaattgcaatttgcaatgaatag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G30000.1 (Glycine max), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactg--tgca---gtatgttgattttctctttccattcat-gttttttttgttcaaatcaactgaaatgaaaatttgattacag
|||||| ||||||||| |||||||| | |  |||||| | || || || || |||||||||||| | ||||| || ||| |||||||||||||| ||   |  || | || |   | ||  ||||    ||| ||| | |  |  |    | | |  |||||| |||   |||  |                       
TCTTCTTGCTATTGCTCAGGAGACCCTAGTGGAGTTCCTTTCCAAAGCTACTGGAACTGCTGTCAACTGGGTCCAGATGATTGGGATGAAGgta-tgacctacttcttcatggtcattgcttgcataaatatattggtataattatattttgcctcattttttctgtcttaatgtag----------------------

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaa--atgaaaatttgattacag----------------
 || ||  |||| || |||||| || | ||||||||| | || ||||| |||||||||||||| || ||||| || ||| ||||||||||||||||   |||  ||  |  ||| ||| |  |   |||  | | |   |||| |||| |   || | | |  | || || |     ||||  ||||||| |                   
ACTCCTTTCTATAGCAGAGGAGGCCCTAGCAGAGTTCCTTTCCAAGGCTACAGGAACTGCTGTTGACTGGGTTCAGATGATTGGGATGAAGgtaatactttc--tg-gcctgaatactcttaaagttgtataatctga-tttctattctttagttgtgtctgaagatgaagttgtttatgattatttgatgaaccttcattgctggtgtag

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag
||||||| | ||||| |||||||||||||| |||||| | |  ||||| ||||||||||||||||| ||||| || ||| ||||||||||||||    | | |  |||    ||   | |    | ||   ||    |  ||   |  |   | ||||  |    ||   |     |    || |        
TCTTCTCTCGATTGCGGAGGAGACCTTGGCGGAGTTCCTTTGCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttt-tagaaaatgttttaatatgtattttcatggttatgtatgtag------

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 5'ss of exon 4
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag-----
||| ||||| || |||||||||||| ||||||||||| |||| ||||| || |||||||||||||| ||||| || ||| ||||||||||||||   |  || ||   |          | |  |   || ||||   |  |   || |  || |    ||||    ||| || ||  |   ||||||| |       
TCTACTCGCAATAGCTGAGGAGACCCTGGCAGAGTTCCTGTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtacaat-ctctttcagc----------ttcctttctttaatttcaccagttgctttaccttgtagcagttc---ccaaatgtaaccatcttttgatttccatgtag

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|58656953|gb|CK045633.1|CK045633
EST:     CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG                         CCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
genomic: CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtatt ... ttgattacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
EST: gi|58661675|gb|CK050355.1|CK050355
EST:     CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG                         CCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
genomic: CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtatt ... ttgattacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
EST: gi|58675209|gb|CK063896.1|CK063896
EST:     CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG                         CCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
genomic: CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtatt ... ttgattacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
EST: gi|58609674|gb|CK037707.1|CK037707
EST:     CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG                         CCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC
genomic: CGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtatt ... ttgattacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGC

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: 39 (upstream exon), 65 (downstream exon)
Score: 8

TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtatt ... ttgattacagCCTGGTCCGGATTCCATTGGAATCATCGCTGTTTCGCACAATTGCAGTGGCGTAGCAGCACGAGCTTGCGGCCTGGTGAGCCTTGAGCCCACAAAG




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