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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatgcttttaatag

Basic information

species Oryza sativa
transcript LOC_Os02g07760.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 9
GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatg-cttttaatag-
|| ||| | ||||||||||||||||||||| ||||||||||||||||  | || ||||||||||||||| |||||||||||||  |   |   ||| ||| | ||   |   |      ||||| |  ||||| ||| | || |  || |||  |||||||  |||||  |   
GGTGCATTGAATGTTGTGATGGGTAATGCTGCTGAGATAGGTGATGCGTTGCTGCAGAGTACACAGgttttatttcctcccatcttgtcttgcatctgcagttttctttgtcttta---taatatgtcaagtaggaatacttgtggttgacactataatataacttttggttag

upper sequence: LOC_Os02g07760.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G128114_T03 (Zea mays), 5'ss of exon 8
GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttcctcccattcttcatcatatccgcaatattagattcttccgagttaataggataagtaagaacaatttttttttacaagataatatg-cttttaatag-
|| ||| |||||||||||||||| |||||||||||||||||||||||  |||| |||||||||||||| || |||||||||||  |   |   ||| | | | ||   |   |      ||||| |  ||||| ||| | |  |  || |||  |||||||  ||||| ||   
GGTGCACTAAATGTTGTGATGGGCAATGCTCCTGAGATAGGTGATGCATTACTGCAGAGTACACAGgt-ctgtttcctcccatcttgtcttgcatctgtacttttctttgtcttta---taatatgtcaagtaggaatactagtggttgacactataatataacttttgattag
















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|218498176|gb|FG949780.1|FG949780
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGC-AAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218492832|gb|FG951181.1|FG951181
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCGACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|88288968|gb|CI520298.1|CI520298
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218492318|gb|FG946726.1|FG946726
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|88519470|gb|CI447124.1|CI447124
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218490731|gb|FG966180.1|FG966180
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|66918914|gb|CX105762.1|CX105762
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
EST: gi|58694576|gb|CK083263.1|CK083263
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCNNNNNNNCTGAT
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGC-AAAAAACTGAT
EST: gi|218491346|gb|FG955033.1|FG955033
EST:     TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAG                         GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG
genomic: TGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATG

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: 65 (upstream exon), 61 (downstream exon)
Score: 17

GGCGCAATAAATGTTGTGATGGGTAATGCTCCTGAGATAGGTGATGCTCTACTCCAGAGTACACAGgttctatttc ... cttttaatagGTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG




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