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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcttccatttgaatttactgaatgctatttccatatgtattgttcgatgttttcttttcaataagtgaattttccttgtagcttcataagaacctgcgaaaaatgggtgatttaatttgtaatttgtatttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTTTACATTCTG

Basic information

species Oryza sativa
transcript LOC_Os03g50480.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 7
gtaagttgctt-ccatttgaatttactgaatgctatttccatatgtattgttcgatgttttcttttcaataagtgaattttccttgtagcttcataagaacctgcgaaaaatgggtgatttaatttgtaatttgtatttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTTTACATTCTG
||||||  |||   ||||    ||  |   | | |||    |  | ||   |||||| ||| |     || | |  || || |||| | | |  || |  |    |  ||     ||||||||||  | |  |      |||||||||||||| |||||||| ||  |||| |||||||| ||| | || || ||||||||||||||
gtaagtaacttgttatttcgtgttttt---ttccattgaagtgagaat--atcgatgctttat-----atcattacatgttacttggatcatgttatgttcacaagggaatctaatgatttaattactgacat-----caattccagGACAATTTTTGACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG
















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|58695799|gb|CK084486.1|CK084486
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58693865|gb|CK082552.1|CK082552
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58675297|gb|CK063984.1|CK063984
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58657583|gb|CK046263.1|CK046263
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58596192|gb|CK006720.1|CK006720
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GAGAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58654844|gb|CK043524.1|CK043524
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTACTGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58682481|gb|CK071168.1|CK071168
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|15008682|gb|AU223070.1|AU223070
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58602722|gb|CK013250.1|CK013250
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGA
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGA
EST: gi|58670270|gb|CK058956.1|CK058956
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58597742|gb|CK008270.1|CK008270
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|29689390|gb|CB685665.1|CB685665
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|58601534|gb|CK012062.1|CK012062
EST:     TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GAGAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: TTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
EST: gi|12622980|gb|AU173193.1|AU173193
EST:     GATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAA                         GACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT
genomic: GATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTT

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: 75 (upstream exon), 62 (downstream exon)
Score: 83

TCGATATTTCTGTTGTAGGTGTCACTACCTTCAGTGGACCTGAAGGCCCTTTTGATGTTGATGTTTTTGACTCTACTATAGATTACATAAAGTTAATGAAgtaagttgct ... ttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTTTACATTCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataagaacctgcgaaaaatgggtgatttaatttgtaatttgtatttaattccagGACAATCTTTGACTTTGAGTCAATTAAAAAGCTTCTGGCATCTCCGAAGTTTACATTCTG
                                           atttaat  putative branch site (score: 83)
                       tgatttaatttgtaat  TA-rich tract