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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaattacatttctttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC

Basic information

species Oryza sativa
transcript LOC_Os01g47080.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
--------------------------------gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaattacatttctttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
                                     |||  | | ||     | |         | |  |  || | |  |||| ||||| ||  |||| ||||||||||||| |||||||| |||||||| ||||||||| ||||||||||||| || || ||| |||||||||| ||||||||||| ||||| |||||||||||||| |
gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9
gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcc--cttttct-----------aattacatttctttc------tgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
|| |||| | | |||| | ||||   |    |   ||||  |||||   |||    ||| ||           |||   |||| |||       ||||||| ||||||||||| |||||||| |||||| |||| |||||||| || || |||||||| |||| ||| || ||||| ||  |||| || ||||||||||
gtttgaaatttaaact-caatgac-tctgacttttttttaatcattgtgttctagttttactgttggtactgaaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 9
--------------gtctg-aactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaattacatttct---ttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
               ||   ||||||||  |    | ||     ||| |   ||     ||   | |     | |||||   ||| |    | | ||||| ||||||||||| |||||||| |||||| |||| |||||||| || || || ||||| |||| ||| || ||||| ||  |||| || ||||||||||
gtttgaaatttaaactcaataactctgactttttttaatcattgtgttctactttactgtt-ggtactgaaatgtaattttttttttgtactatatagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTCGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9
------------------gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaa---ttacatttctttctgt-------agAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
                  ||    |   |||  |    | |||  ||| |||  |||| ||||| ||||  ||   || |   ||  |||| ||| |||       |||| ||||||||||| ||||||||||||||| |||| |||||||| ||||| |||||||| |||| ||| || ||||| || || || || |||||| |||
gtttaagtcaatctatttgttgccatgttgactttttgt-ataatcctttgcactttc-tcatttaattgtctgacctgaaatttgtatttttttttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 9
------------------gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaa---ttacatttctttct------------gtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
                  ||    |   |||  |   ||  || |||| |||  || ||||||| ||||      ||| |   ||  ||||  || |            |||||| ||||||||||| ||||||||||||||| |||| |||||||| |||||||||||||| |||| ||| || ||||| || || || || |||||| |||
gtttaagtcactctatttgttgccatgttgactttttatt-taaccctttgcactt-cctcatttaattgttagatctgaaatttgtattttatttttttggattcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACTCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9
---------gtctgaactc--tgaactgccatgatacccc--tgtgccttttcctcattcaattcccttttctaattacatttcttt----ctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
         | ||||  ||  ||   ||  |   | | ||  || | || ||  | ||  ||| |    |   ||  |||||| |||    ||  |||| || |||||||| ||||||||||||||| |||| |||||||| ||||| |||||||| |||| ||| || |||||||| || || || ||||| ||  
gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatctaatccaaaataacaagaacatttttttgctactacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------gtctgaactctgaactgccatgat--acccctgtgccttttcctcatt-----caattcccttttctaattacatttctttct--gtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
                                                         | | |  | | ||     |   |  |    ||| |    |  | | |     ||||      ||   || |  || ||||||  |||||| || ||||| ||||||||||| | |||| |||| ||||||||||| |||||  | || ||||| || |||||||| || || || || ||||||||||
gtcatttaacatatcctttatatttattttaatgctgcattggccttgtttttgtaatgtaattttttaaaaaaaaaagtttaaatttgtactccattttaactgctaacaatgaatacttaccataagcttcctttctctgtagAACCATATGAGCGAAATGTTTGCTTTCCATGCAACCATGATGTCCAATACTCTCAGTACTTCAATAGTTGTTTTCACTAGAACTGGTTTCATGGCTATCC

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|58683676|gb|CK072363.1|CK072363
EST:     CCACTATGTCTGGTGGGGAAACACCGGCTAACCTTGGTCAGGTGTTCAAG                         AATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACT
genomic: CCACTATGTCTGGTGGGGAAACACCGGCTAACCTTGGTCAGGTGTTCAAGgtctgaactc ... ctttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACT




















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: 69 (upstream exon), 75 (downstream exon)
Score: 31

TCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGAAGCCACTATGTCTGGTGGGGAAACACCGGCTAACCTTGGTCAGGTGTTCAAGgtctgaactc ... ctttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctgtgccttttcctcattcaattcccttttctaattacatttctttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC
                               ttctaat  putative branch site (score: 31)
                        ttcccttttctaatta  CT-rich tract
                             ttttctaattacattt  TA-rich tract