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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact...

Basic information

species Oryza sativa
transcript LOC_Os01g47080.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggct--gattttttttattttttattcagtcatact-
||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||| ||||||   |||||||||| || ||||||||||| || |||||||| | ||  ||| ||| |   |  |     | | |  | || |    ||  || |||| |  ||||   |   ||   |       |     | | |  
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcacatgttttgctttttgctcaaaagaaattgatgttattag---ttgttagctaagggtggctccaagagttagcaagccagctcataacttgcca

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G30430.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata-tccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttatt-cagtcatact
|||| || || |||||| |||| || || || || ||||| || ||||||||||||||||||||||  || |||||||||||||||||||| || |||||||| || ||| | |  | | |     |     || ||           |  ||     | |  |||   || |        |     |||  || ||| | |
TTCACCCGACACCAACCAGAGCCGAGGTATCCGATATTGCAATTGCTGTTCGAGAAGGTTCTGATGCAATAATGCTTTCTGGGGAAACTGCTCATGGAAAgtaagtaataattccatgcctcaaagtgtccaattaccttggcaggtgatgttctcctatttgagtt--cttacaaaggacaggaaatatcacaatcaaatt

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G28980.2 (Glycine max), 5'ss of exon 8
--------------------------------------------------------------------------TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact
                                                                          |||| |||||||||||| ||||||| || ||||| || || || || ||||| |||||||||||||| || ||| | ||||| ||||| || || |||||||| || | ||  ||||| |  || ||                                                                         
AGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAGAGgtatcagatatagcaattgcagttcgtgaaggttctgatggaataatgttgtctggagaaacagctcatggaaagtaagtaa-atagttttcctgcgccta-------------------------------------------------------------------------

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA09G23150.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact-
|||| |||||||||||| ||||||| || || || || || || ||||||||||||||||||||||| || ||| | ||||| ||||| || || |||||||| || |     ||| |||   |     ||  || | |     |||   | || ||     || | |   ||   |||| |     ||   | | |    
TTCACCCAACTCCAACCAGAGCAGAGGTATCGGATATAGCAATTGCTGTTCGAGAAGGTTCTGATGGAATAATGTTGTCTGGAGAAACAGCTCATGGAAAgtaagtaaatagttttccttcccctatagtgtccaattattcagtcactttatattactagtagcatgtatatgactttt-tggcaaatctgggctttgaa

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G37210.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata-tccttttcttatgcatagatgatcactcacatgatcaaaatt-taataactaaagtag-gctgattttttttattttttattcagtcatact
|||| ||||| |||||| |||| || || || || ||||| || ||||||||||||||||||||||  || |||||||||||||||||||| ||||||||||| || ||| | |  | | |     |     || ||         | | ||| | |||  | |  |    |  |        |  |   | |||        
TTCACCCAACACCAACCAGAGCCGAGGTATCCGATATTGCAATTGCTGTTCGAGAAGGTTCTGATGCAATAATGCTTTCTGGGGAAACTGCTCACGGAAAgtaagtaataattccatgccttgaagtgtcctattaccttggcaggcgatattctcatatttgagttcttacaaaggacaggaaaatcacaatcaaatgc---

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G28980.1 (Glycine max), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcataga-----tgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact
|||| |||||||||||| ||||||| || ||||| || || || || ||||| |||||||||||||| || ||| | ||||| ||||| || || |||||||| || | ||  ||||| |  || || |       || |||   |    |     |||  |  |   |   | | |         |||   | | ||||     
TTCACCCAACTCCAACCAGAGCAGAGGTATCAGATATAGCAATTGCAGTTCGTGAAGGTTCTGATGGAATAATGTTGTCTGGAGAAACAGCTCATGGAAAgtaagtaa-atagttttcctgcgcctaaagcatccaattactttgaaaggctggtcttagaagtttgtgactggtaaggggaccattttaccactaagtcc----

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcata--gatgatcactcacatgatcaaaatttaataactaaagtaggc-tgattttt---tttattttttattcagtcatact
||||||||||||||||||| ||||| || |||||||||||||| |||||| |||||||| ||||||   | |||||||| || |||||||| ||||||||||| |||  |   | || | ||| |      ||||    |  || ||    ||| |||   ||   || || ||| | |    |||| ||  ||| |||       
TTCATCCAACTCCAACCCGGGCAGAGGTCTCAGACATTGCTATCGCTGTTAGAGAAGGTGCTGATGCGGTAATGCTTTCAGGAGAAACTGCTCACGGAAAgtaagtggcagtatcttttcatgtactctattgatttagcttataat-ggcattgaatgtttattatatgcatgaatctcaactttacttgatat-cag-------

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtca-tact-----
|||| ||||| |||||||||||||| || ||||||||||| || ||||| ||||| ||| ||||||   ||||||||||||| |||||||| || |||||||| |     || || ||||     |    | ||  | | |||   |       ||||    || |   || ||  | ||       |     |    |||     
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagc----tctttctcttggagtttctagttccttaagatg--tagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtg-----atatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcatact
 ||| || || || || ||||||||||| |||||||| || || ||||| || |||||| | ||||  ||||||||||| |||||||| || || |||||||| | |     | | |  |    |||   | ||   |   |           || | |||   |    |  |   ||  | ||  | ||     |  ||     
CTCACCCTACGCCCACACGAGCAGAAGTCTCAGACATAGCCATCGCTGTCCGTGAAGGTGCGGATGCAATTATGCTTTCAGGGGAAACCGCTCATGGAAAgtaagcgcgattaaaccagtgcactatctctcgacagtttttttttctgcttgaagtaaatttttgtgtttcgaatatcgtattactgttgaggacgatc-----

upper sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtcat-act-
 ||| || ||||| || |||||||| ||||||||||| ||||| || || || |||||| | || |   ||||||||||||| ||||| || ||||||||||| || |  |       || |  |||| |  ||  | | || ||| ||  | |    | |      ||  |  ||||      |        || | | | 
CTCACCCCACTCCCACACGAGCAGAGGTTTCAGACATAGCTATTGCCGTCCGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagt-acctttggaatttgttgatag-tcttctttaatatcatctaagctcatagcccagtaactgccaaaattttggggcatcaggcttatcgtcagtg

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|58599601|gb|CK010129.1|CK010129
EST:     CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAA                         GTTTCCTTTGAAAGCTGTTAAGGTCATGCATACT
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACT
EST: gi|2309639|gb|C25794.1|C25794
EST:     CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGGAACTGNACACGGAA-                         GTTTCCTTTGNAAGCTGTT
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTT
EST: gi|58683676|gb|CK072363.1|CK072363
EST:     CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAA                         GTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGA
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGA
EST: gi|58668249|gb|CK056935.1|CK056935
EST:     CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAA                         GTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGA
genomic: CGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGA

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: 52 (upstream exon), 67 (downstream exon)
Score: 34

TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgata ... ttcctggcagGTTTCCTTTGAAAGCTGTTAAGGTCATGCATACTGTTGCCCTGAGAACTGAAGCCACTATGTCTGGTGGGGAAACACCGGCTAACCTTGGTCAGGTGTTC




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