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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctatttatttgtgtcaatattttcatccgatttagtttattgctatgttcgcagaacacattcttattatgtcagtacgttattcaaatctag

Basic information

species Oryza sativa
transcript LOC_Os03g44900.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G340749_T01 (Zea mays), 5'ss of exon 4
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctattta----------tttgtgtca-atattttcatccgatttagtttattgctatgttcg--cagaacacattcttattatgtcagtac-gttattcaaatctag---------------------------------------------------------------------
|||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || |||  ||| || ||           | ||  ||  | ||  |    ||    |  | |   |||  || |  | |          ||||||     | |  || || ||  |||                                                                      
ATTGGAGTCAATCTTGAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTCAATGATGTTAAAGATTTTCTTGATGATTATGTTGAACGTAATCAGgtatgtctgccttcatagttgaccctcatactctgcatcccaaatcataggtcgtccaaaatgacctctaatttggaacggggagggggagtattatcctttttctattgttgaatgctaattgtgataacgtacagacatatgatcggccttttatttgttattttttgtttttttcgctcatgtttag

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AC197122.3_FGT003 (Zea mays), 5'ss of exon 7
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctattt-atttgtgtcaatattttcatccgatttagtttat------tgctat---gttcg---cagaacacattcttattatgtcagtacgttattcaaatctag--------------------------------------------------------------------
|||||||||||| ||  | ||||||||||||||||||||||||||||||||||| |||||||| |||||||| || |||||||||||||||||||| ||||| || |||  ||| || || | |  ||         || |    | ||| ||||      ||  ||    || |   | |       |  |||  | |   |   || || |   |||                                                                     
ATTGGAGTCAATCTTGCGGCTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTCAATGATGTTAAAGATTTTCTTGATGACTATGTTGAACGTAATCAGgtatgtctgccttcgtagttgactcatgctctctccatcctgaattataggttatccaaaatgacatctaatttggaacggggagggataatatcctttttttgtattgttgactgctaattgtgataacatacaggcatatgatcgaccttttatttgttattttcgttttcttcattcatatttag

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G26850.1 (Glycine max), 5'ss of exon 6
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctatttatttgtgtcaatat--tttcatccgatttagtttattgctatgttcgcagaacacattcttattatgtc--agtacgttattcaaatctag------------------------------------------------------------------
||  || |  || || || ||  | |||||||||||  | ||||| ||||| ||||||||||| ||||||||||||||||||||||| || ||||| ||||| || || |  |    |  | |  || || | |  ||| |    ||  |   |||  |   |       | |   |   || |   |   |  |   | ||  | | |                                                                    
ATGTGAATTTATCTTGAGGCTACTAGATAATGATGAACTAAGTCCAGAGCAGGTTAATGATGTCAAAGATTTCCTGGATGACTATGTAGACCGTAATCAGgtttgtcttttatagcttgcactcttgccattttgcttttaaaaaataaaaactatcaccgaggaaatttaccctttgtgtagtcctttcaaagaaagtcttagagtttgataccatgcaaaaattatgaattggtattaattttctgtctttcctatttttcattttattttacag

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 6
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggct-gtattcctatttatttgtgtcaatattttcatccgatttagtt--tattgctatgttcgcagaacacat-tcttattatgtcagtacgttattcaaatctag-------------------------------------------------------------------
||  || |  || || || ||  | |||||||||||  | ||||| ||| | ||||||||||| || |||||||||||||||||||| || ||||| ||||| ||||| ||||  || |  | |  || || | || |  |   |  ||     |||  |   ||      | |   | | || |  | |||    |    | | |  | |                                                                   
ATGTGAATTTATCTTGAGGCTACTAGATAATGATGAACTAAGTCCAGAGGAGGTTAATGATGTCAAGGATTTCCTGGATGACTATGTAGACCGTAATCAGgtttggcttgtatagct-tgcactcttgccatttttcttttaaaaaataaacactatcaccgagtaattttaccctttgtattgtcctttcaaagagagtcttagagtttgataccatgcaaaatttatgaattggtattaattttctgtctttcgtatctttcattttattttacag

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G04690.2 (Glycine max), 5'ss of exon 6
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctatttatttgtgtcaatattttcatccgatttagtttattgctatgttcgcagaacacattcttattatgtcagtacgttattcaaatctag
||  || |  || || || ||  | ||||||||||| || ||||||||| | ||||||||||| ||||||||| |||||||||||||||| ||||| ||||| || || | |    ||   | ||  | || | ||  |  |   | |||  ||    |||||  |||| |  ||   ||  |||  ||   |  |  ||||  |  
ATGTGAATTCATTTTGAGGCTACTAGATAATGATGAATTAAGTCCTGAGGAGGTTAATGATGTCAAAGATTTCTTGGATGACTATGTTGAGCGTAATCAGgtttgtct-tttagaaatcattctgcttaaaaaattggacac--ctgagtaaatgttgatgttt-cagacc-tatgtatagcatggaagagtgagaaacaaaaat--

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 5'ss of exon 6
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctatttatttgtgtcaatattttcatccgatttagtttattgctatgttcgcagaacacattcttattatgtcagtacgttattcaaatctag---------
 |||||    || || || ||| |||| |||||||| || ||||| || ||||| ||||| || |||||||| |||||||| ||||||||||| || ||||| || || |||    ||     ||    | | |  | ||  | | ||   |     |        | || ||| |  |||||| |  ||||  | || || | |           
GTTGGAACTGATCTTGAGGCTTCTGGACAATGATGAATTAAGTCCAGAACAAGTAAATGACGTCAAAGATTTTCTGGATGATTATGTTGAACGAAATCAGgtctg-ctatatctaaatc---ctggaatattttgcttatgtgttataccctgggtttcgaacattaaaatacacttatattatctt-gtactgtgtttaactttcttctatgtag

upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 5'ss of exon 6
ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgtattcctattta--tttgtgtcaatattttcatccgatttagtttattgctat-gttcgcagaacacattcttattatgtcagtacgttattcaaatctag
 || ||    || || || ||  ||||||||||||| |||||||||||||| || |||||||| ||||| ||| ||||||| ||||| |||||||| ||||| |   |   |     ||||  ||||| ||  ||||||| |  ||  |||  |    || |     |||  | | |||   | ||  |   | | ||            
GTTAGAACTGATTTTGAGGCTACTGGATAATGATGAATTGAGTCCTGAGCAGGTCAATGATGTAAAAGACTTCTTGGATGATTATGTGGAACGTAATCAGgtttaagttgctcgaactttaattttgtttctttattttcctt-gacatagcctgccacttttagatgcaacatatattaagagtacatgcatgcattgcc---------

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|58673547|gb|CK062233.1|CK062233
EST:     GTTGAACGT-ACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: GTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
EST: gi|66918088|gb|CX104936.1|CX104936
EST:     AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
EST: gi|29667065|gb|CB663340.1|CB663340
EST:     AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
EST: gi|29645498|gb|CB650505.1|CB650505
EST:     AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
EST: gi|117216962|gb|CT845285.1|CT845285
EST:     AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
EST: gi|29638285|gb|CB643294.1|CB643294
EST:     AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
EST: gi|29630458|gb|CB635467.1|CB635467
EST:     AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAG                         GAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT
genomic: AAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCT

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: 56 (upstream exon), 75 (downstream exon)
Score: 22

ATTGGAGTCAATATTAAGACTTTTGGATAATGATGAGTTGAGTCCTGAGCAAGTTAATGATGTGAAAGATTTCCTGGATGACTATGTTGAACGTAACCAGgtgtggctgt ... tcaaatctagGAAGATTTTGATGAATTTAGTGATGTGGAAGAGCTCTATAGCACATTACCTATGGAGAAGGTTGAAGCACTAGAAGACATGGTTTCACTTGCCCCTTCCA




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