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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag

Basic information

species Oryza sativa
transcript LOC_Os05g03820.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgt-----gcagtgcatccctgtattaacttcttgcttta--tttgattttcacttatg-atttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| |||||||||||||| || || |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||||  |      || ||||| |||     | | |||| |   |  | |||| ||   || ||  | |   ||||    || || | |||  | |||| |                                                   
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATCTTTATCAGgtaacttctcttacattgcattccttgtacagcatcttacagaaactatgatcttagtttgtgtgtgttaccattcttttgtcagagataa-tacagtacc--------------------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| |||||||||||||| || || |||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| |||||||| || |||||||           | |   |  | || | ||  |||   ||    ||    |  | ||  |   |   |   | | | | | || | |    |   | |    |   |                                 
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATCTATATCAGgtaac----------ttctctttctgacgttttcttttccctgtgcatcttgcagaaattatga--tcttagctcgtgtgtgtttttacttgacattatataagactgacca-------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G02570.1 (Glycine max), 5'ss of exon 2
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgca-tccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
||| || ||| |||||||||| ||||| ||||| |||||||||   ||| |  ||||||| ||||||||||||| |||| | ||||||||||| || ||||| | || | ||||| ||  ||   ||||      | | |  | | ||| | | || |||| |    |    | |  |  | |  |  ||   | ||  | ||                                         
AAGTATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATCTCTATCAGgtca-gt-ctgtgcaatctttggcataacaagaatcctaagat-agtttaattcataattt-catcctattttactgttaaaagttgaagcatgcaatgtgtta----------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G42900.1 (Glycine max), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgca-tccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| ||| |||||||||| ||||| ||||| |||||||||   ||| |  ||||||| ||||||||||||| |||| | ||||||||||| || ||||| | || | ||||| ||  ||    |||      | | |  | | ||| | | || |||| |   ||    | |  |  | |  |  |    | ||     |                                         
AAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATCTCTATCAGgtca-gt-ctgtgcaatctttggcacaacaagaatcctgagat-actttaattcataattt-cattttattttactgttgaaagttgaaacatgcaatgcaatg----------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
 ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||  || ||||| |||||| |      | |     |  ||||||||     ||| ||||   ||      ||||||| | |||   |||| ||  |||| |||  | || |    | | |  || || |||                            
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACCTTTATCAGgtact---tgtttcgctgatacattaactt-----tttttttgccattaga--gtgatttg-gaatttttatgcaat-catattttc--tacggataaatatgtatcatca-ttg----------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
 ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||| || ||||| |||||| |      | |     || || |||   ||  | | |||     |      |||||||    ||   | || ||  |||| |||        | | | | |                                       
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACCTTTATCAGgtact---tgtttcgctgatgcataaaccattttttcttttttgccattgga-gtgatttgaaattttttacgcgat-catattttctacagatgaatatgtata--------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||||||||| |||||||| |||||||| || ||||||||||| |||||||| || || ||||||||||||||||| ||||||||||||||||| |||||||| |  |    |    |     |   |||  |  ||     |    | | |  |  |    |  |  ||| || |                                                                 
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatctacgg--atgtcacag----------------------------------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| ||||| |||||| | ||   | | || |  | || |  |  | ||||  |   |    ||  | ||| | | |||    ||   ||| ||| || || |   | |  |                                            
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtact-tgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgat--tata-ataactccaataaaataactaaaag---------------------------------------

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 3
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag
|||  | ||  | ||||| ||||| ||||||||| | ||||| || ||||| || ||| | |||||||| || || ||||||||||||||||| || ||||||  | |   ||    |||   || |  |     | |||     ||| | | || ||       | | ||     | | ||  || | |      | |                                            
AAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGAGCGCCTCTGGAGACACTTCATCAAACATGCGCCGAGGTCAATTCACATCTGTATCAGgtatggcgggttgtccaccttctttcatgtgaatatatataaagattttaatcat-atcgtaatctggtcacat--tttgtaattttatttttggggctggac----------------------------------------

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|7219950|gb|AU063307.2|AU063307
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|33796283|gb|CF324008.1|CF324008
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|88347509|gb|CI637449.1|CI637449
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGG
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGG
EST: gi|88573359|gb|CI664930.1|CI664930
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTG
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTG
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|88336064|gb|CI647258.1|CI647258
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAA
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAA
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT

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: 73 (upstream exon), 71 (downstream exon)
Score: 192

AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG




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