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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaacttcttgatattttgatcttgcactcacttgagactctaattgagatcacacttggaactcagttggaaagttttttattttgtaccatgcta...

Basic information

species Oryza sativa
transcript LOC_Os02g17320.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 10
GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaacttctt------gatattttgatcttgcactcacttgagactctaattgagatcacactt--ggaactcagttggaaagttttttattttgtaccatgcta
| || ||||||||||| || |||||||||||||| |||||||||||||||||||| || |||||  ||||| |       ||||||||  || |   |    || ||  |||||| ||| | |   ||  || |||||  |    ||      ||    |         
GGTCTGTTTACACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTATCTCAGTGATCAGGAGgtaccaacttttcctaaacgatattttcttcatatgcctgttt-aggttctaatcgagttaatgatttaggcactcacataaggagggggaaatgagcttt-------

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 5'ss of exon 12
GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaacttctt------gatattttgatcttgcactcacttgagactctaattgagatcac-acttgga-actca-gttggaaagttttttattttgtaccatgcta
|||| ||||||||||| || |||||||||||||| ||||||||| |||||||||| || |||||  ||||| |        |||| ||  |  |   ||   || ||  |||||  ||| | |  |||| |  |||||     | | |        | ||||        
GATCTGTTTACACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAGgtaccaacttttcctaaacaatatattctttgtatgcttgttt-aggttctaaccgagttaatgacttaggcactcacaaaaggaggaaaaaggctatgta--------
















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|86902718|gb|CI306521.1|CI306521
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTG
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTG
EST: gi|3760815|gb|C98069.1|C98069
EST:     CTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAA
genomic: CTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAG-AAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAA
EST: gi|87029276|gb|CI276544.1|CI276544
EST:     TCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: TCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|12623049|gb|AU173262.1|AU173262
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGGGTGGTATCTCAGTGATTAGAAG                         TGGGGAGAGTTTGGANAATGCATTGNGGGCATGCTG
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTG
EST: gi|29675373|gb|CB671648.1|CB671648
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|29627016|gb|CB632027.1|CB632027
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|66922909|gb|CX109757.1|CX109757
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAACGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT

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: 67 (upstream exon), 75 (downstream exon)
Score: 13

GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG




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