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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTATGGGTTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatattactgtaattgatatatttcttaggatgtgtttagaagggagataggctttggagttttgttatttttaacatattcacaggctgttattt...

Basic information

species Oryza sativa
transcript LOC_Os03g58960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G027307_T01 (Zea mays), 5'ss of exon 3
GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTATGGGTTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatattactgtaattgatatatttcttaggatgtgtttagaagggagataggctttggagttttgttattt----ttaacatattcacaggctgttattt
||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||| ||| |||| ||  ||||||||         || ||   ||||  |||| | | || | ||||     |||    || |   ||| |   | ||||    
GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATTGTGTTGGGGCACTGAACTACAAATACTTTCTTCTGTTCCTGgtataatactactatacctgatatatgctcctttttgagta-ggaagatagattgacctttgggtttcaaagtttgtggttgatgcattaatgaggtgttt---

upper sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G001265_T01 (Zea mays), 5'ss of exon 3
GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTATGGGTTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatattactgtaattgatatatttcttaggatgtgtttagaagggagataggctttggagttttgttattttt--aacatattcacaggctgttattt
||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||||| ||| |||| ||  ||||||||         || ||   ||||  |||| | | ||  |  || |  | |  |  || || | |  | | ||||    
GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTTGTTAATTGTGTTGGGGCGCTGAACTACAAATACTTTCTTCTCTTCCTGgtataatactactatacctgatatatgatcctttttgagta-ggaagatagattgaccttaaatcttggccagtggtggaagatgtccctatgttgttgca-
















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|29659672|gb|CB655947.1|CB655947
EST:     TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
EST: gi|27577344|gb|CB000039.1|CB000039
EST:     TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
EST: gi|58685848|gb|CK074535.1|CK074535
EST:     TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
EST: gi|29659673|gb|CB655948.1|CB655948
EST:     TGTTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TG-TTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
EST: gi|218500781|gb|FG951176.1|FG951176
EST:     TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
EST: gi|27554328|gb|CA998228.1|CA998228
EST:     TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
EST: gi|29675562|gb|CB671837.1|CB671837
EST:     TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTG                         TTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC
genomic: TTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCAC

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: 70 (upstream exon), 68 (downstream exon)
Score: 21

GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTATGGGTTGTTAATTGTGTTGGGGCACTAAACTACAAATACTTTCTTCTCTTCCTGgtatgatatt ... ttccatgcagTTTTACACCTTCCTTGAGACAACACTGGTTACCCTTTCTCTATTGCCTCACTTCATAGCCTTCTTTAGTGATATTGATATCCCAGGAAGTCCTGCAGCAC




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