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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCATTTACAACCTTTAACATGTACTGGGAGAAGTGCATGGAATTACCTATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtggctagtggcctaccattatttatcttttttatttttgaagattttctatgtttttaatttgtctgtacttacagaattatctctagatta...

Basic information

species Oryza sativa
transcript LOC_Os02g41550.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G172152_T01 (Zea mays), 5'ss of exon 3
CTTGCATTTACAACCTTTAACATGTACTGGGAGAAGTGCATGGAATTACCTATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtggctagtggcctaccattatttatcttttttatttttgaagattttctatgtttttaatttgtctgtact-tacagaattatctctagatta---------
|  ||||||||||||||||||| |||||||||||| || |||    ||||||||||   |||||  |  |||||||||   |   ||||| | |  |||||||  |  | || |      || ||| ||||    |||| ||    ||  || |     |||||| |||| |||| | |  | ||| || | | ||| ||          
CAGGCATTTACAACCTTTAACAAGTACTGGGAGAAATGTATGAGCCTACCTATTGAGATATCACAATATCTTGCACCTACAAGGCTGGTGGCAGCGCCAGgtaactttttgcca------tagcatcattttctgttttcat----gagcatctgtacagttttttatttatctgcattacatagatttgtttttagttttggttcctca
















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|29674937|gb|CB671212.1|CB671212
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29629647|gb|CB634656.1|CB634656
EST:     TATTGACGTATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTANGACTTGAAT
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAAT
EST: gi|29671259|gb|CB667534.1|CB667534
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29627388|gb|CB632399.1|CB632399
EST:     TATTGACGTATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29641884|gb|CB646891.1|CB646891
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
EST: gi|29668745|gb|CB665020.1|CB665020
EST:     TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAG                         GTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA
genomic: TATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAA

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: 60 (upstream exon), 65 (downstream exon)
Score: 14

CTTGCATTTACAACCTTTAACATGTACTGGGAGAAGTGCATGGAATTACCTATTGACGCATCACCGTCACTTGCACCTTGGAAATTGGTGCCTGTCCCAGgtagatcgtg ... tgacattcagGTTTGGAGAGTGTTCGTAGCTGTTCTGTTGATGACCTAGGACTTGAATCAAGCAAGGATGAGGAATCAAGTAATGCTTTGCTAATGAGGGCCTGGTCTCC




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