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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 21
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatga-ttctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
| || |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||||| ||| ||||||||    || ||   ||  |||   ||  |    ||  | | |        ||    || |   | |||||   |       |||                      
TTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtttgaattctttat----tcctggggtctgcaaagtgacaagtttcacattccctt---tttaagtggat-cacatctgtttgaatatgtgtatcag---------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G111355_T02 (Zea mays), 5'ss of exon 2
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
||||||||||||| |||||||||||||| || ||||||||||| || ||||| ||||||||||| |||||||||||  | ||||||||||| |||||||||| || || || ||||  ||     || |  |  || ||  || | | ||      ||  | |     ||| |   |  |  | ||| | |  ||||| || | |             
TACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCCTCCCTGTTGAGCCTTTGGTTGATGAATGTGAGAAGAGgtttg-tttttcatatcctcccagtttacttattcacat-gagtgaaggta-----gccaagatgtgcatg-tccataatgctcttggtaaaatcatcattgacag------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
|  | |||||||| |||||||| ||||||||||| ||| | ||||| || || |||||||| ||||| ||||||||  ||||||| ||||| |||||||||| ||    ||| |   | | || || ||  ||  |   ||      | |       |||      ||  ||                                              
TGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTCTTCCAGTTGAGCCTTTAGTTGAAGAATGTGAGAAGAGgtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttc-tatgcgcag--------------------------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccag-attaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
|  | |||||||| |||||||||||||| || || ||| | || || || || || |||||||| || ||||||||  ||||||| ||||| || ||||||| || |  |||   |     | | || ||   |||| ||    |  |||| ||            ||| | |||||||  |   | |                               
TGTTAGATGATGAATGCCCTGAAGATTTTATCAAAGGTCTTATACTTTCAGTTCGCTCTCTCCTGCCAGTTGAGCCTTTAGTTGAAGAATGTGAAAAGAGgtgtgctagttt---tctctctattttgcatctccagtatcgttgctatgttcatttct-------catgttctttttttatgcatag-------------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 20
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
|| | |||||||| |||||||||||||||||||| ||| | || || || || |||||||| ||||| ||||||||  ||||||| ||||| |||||||||| ||    ||| |   | | || || ||  ||  |   ||      | |      ||||      ||  ||                                              
TATTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTTATACTTTCAGTTCGTTCTCTTCTTCCAGTTGAGCCTTTAGTTGAAGAATGTGAGAAGAGgtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcattgcactttc-tatgcgcag--------------------------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
|  | |||||||| |||||||||||||| ||||| ||| | || || || || ||||||||||| || ||||||||  ||||||| ||||| ||||||||||  |  ||| ||| ||   |     ||||| | ||  ||   | ||||| ||        |  |  ||   |||| ||  | |                                  
TGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCCTGCCAGTTGAGCCTTTAGTTGAAGAATGTGAGAAGAGgtgcgtctctctatctttcatc----tccactatca--tt---gccatgttcattt-----ctcatttaattttttatgcatag----------------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
| ||||||||||| |||||||||||||| || || ||  | ||||| ||||| |||||  | ||||||||||| ||||| || || ||||| ||||||||||   || ||||   | ||| ||  || |      | |||| |    | |      | | ||    |||||  ||| || ||| |                                 
TGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGCTTCCTGTTGAACCACTTGTCGAGGAATGTGAGAAGAGgtg-aatccttttggtcatcctggtttgcgttcata-attatgtctgtttagttctggaaactctaatatg--tttctgctttttcag------------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgat-tctttatat-tatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
| || |||||||| |||||||||||||||||||| ||| | ||||| || || || ||||| |||||||||||||| || || || ||||| ||||| ||||    | | ||||  | | |   || |||||  |  |  || |   | | |   |   |     | ||| |  | |||||||| |  |                               
TTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTCTTCCTGTTGAGCCCCTCGTGGAGGAATGTGAGAAAAGgtgcattgtttttacctgtgtaccgt-ttccattaatatttttaattcttat-tgctttcgttttatcattttgtgttttgttt-gcag-------------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgt-atgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
| || |||||||| || || |||||||||||||| ||| | ||||| |||||||| || || |||||||||||||| || || |||||||| |||||||||| |||  ||  ||          ||| ||     | | || |     | |  ||     ||    | ||||||||    | | |||                                
TGCTAGATGATGAATGTCCAGAAGATTTCATTAAAGGTCTAATTCTTTCTGTCCGGTCGCTGCTTCCTGTTGAGCCCCTTGTGGATGAATGTGAGAAGAGgtgatgtgtccctac-------catatgccctgttcgggttcactttctttttactt---caattgcttatgctttgc-atgtggttttcag---------------------------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 22
TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcag
| ||||||||||| |||||||| || |||||||||||||||||  | || ||||| || || ||| |||||||||| || ||    || || ||||||||||| |    |  ||  ||  || |       || ||  ||  | ||       || | | |  ||  || | | || |  |    | |  |   | |  || || | |        | 
TGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGCTTGCTGTTGAGCCTCTGGTCACCGAGTGTGAGAAGAGgtacg---ttgaatgctagtttttg------aatca--ttgtgagc-------catgtagatgaatttacgttgttcttgtcaagtacaaattgccttgttaatttgttcaccagtac

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|58652712|gb|CK041392.1|CK041392
EST:     CCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGCAAGAG                         GAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGG
genomic: CCTTCCTGTTGAGCCACTAGTTGATGAATGCGAG-AAGAGgtatgattct ... cttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGG
EST: gi|87006844|gb|CI285878.1|CI285878
EST:     GTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAG                         GAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGG
genomic: GTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattct ... cttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGG

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), 71 (downstream exon)
Score: 61

TACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCCTTCCTGTTGAGCCACTAGTTGATGAATGCGAGAAGAGgtatgattct ... cttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC




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