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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTGATGCATTCTCACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaactctctttagcacaaaacatttcttcaaatgacgcattttcggagttctgtctgaaacattatagcttcaggtgaactcacatgttgtcttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g17240.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17240.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G092793_T01 (Zea mays), 5'ss of exon 8
GGAACTGATGCATTCTCACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaactctctttagcacaaaacatttcttcaaatgacgcattttcggagttctgtctgaaacattatagcttcaggtgaactcacatgttgt-cttgcag-
|||||||||||||| || ||||| |||||||||||||| || |||||||| || |||||||| || ||||||   ||      |  | | | |     | |  | | |||       | || |  |   |  ||| | |  |        ||   |  ||   | |   | 
GGAACTGATGCATTTTCGCAGTCTGGTCTATACTCAAACCATCAAGATATAGGCCCTCGATATGCAgtaatctcttcctccatgttctatagaacgtcttatgtcatgca-----aaacttataacctcattattcttgtgtgcaaaattctggaaccttaaacatatggg

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv06s0004g06220.t01 (Vitis vinifera), 5'ss of exon 8
GGAACTGATGCATTCTCACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaa---tcaactctctttagcacaaaacatttcttcaaatgacgcattttcggagttctgtctgaaacattatagcttcaggtgaactcacatgttgtcttgcag-
||||||||||||||||||||||| ||| |||||||||| || |||||||| |  ||||||||  |||| |   | ||| || || || |      |      ||  | | |  |  ||   |  |  |    || ||  | | | |   |    |      |||  | |  | 
GGAACTGATGCATTCTCACAGTCTGGTTTATACTCAAACCATCAAGATATTGCCCCTCGATATTCTgtgagtattaacact-ttcagtattgt-taccataccagttaatgtttgctcat-gcacaattc--aatatcgtggttgctcat--ctttggggtttgagtggtggg
















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|29656074|gb|CB652349.1|CB652349
EST:     CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCT                         GGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
genomic: CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
EST: gi|58594059|gb|CF992367.1|CF992367
EST:     CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCT                         GGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
genomic: CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
EST: gi|33679924|gb|CF308163.1|CF308163
EST:     CACAGTCCGGTCTATACTCAAATCACCAAGATGTCGGTCCTCGATACGCT                         GGTGTACTGCTTGGTCTTTCTA-CACGGCTGGGGTTTTAGCTGGTG
genomic: CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTG
EST: gi|66923063|gb|CX109911.1|CX109911
EST:     CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCT                         GGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
genomic: CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
EST: gi|29678015|gb|CB674290.1|CB674290
EST:     CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCT                         GGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
genomic: CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTT
EST: gi|218504692|gb|FG962736.1|FG962736
EST:     CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCT                         GGTGTACTGCTTGGTCTT
genomic: CACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTT

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: 66 (upstream exon), 65 (downstream exon)
Score: 31

GGAACTGATGCATTCTCACAGTCCGGTCTATACTCAAATCACCAAGATATCGGTCCTCGATACGCTgtaatcaact ... tgtcttgcagGGTGTACTGCTTGGTCTTTCTAACACGGCTGGGGTTTTAGCTGGTGTGTTTGGCACAGCGGCAACAGGATACATCTTGCAGCATG




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