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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgtattgatccatgcattttagtgaaaactgcacataactttgcattacactgattgaattccactcaagcagGTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAAGGGTCATTGCAGACCATTCTGCAACTGGGGCTATGGATTGTGATAAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g38270.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------------------------------gttgtgta-ttgatccatgcattttagtgaaaact-gcacataactttgcattacactg-attgaattccactcaagcagGTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAAGGGTCATTGCAGACCATTCTGCAACTGGGGCTATGGATTGTGATAAAAG--
                                                                                                        || || |     |  | |  ||||  ||   | |   | | || ||  || ||      ||| | |||       ||||  |||||||| |  ||||||||||||||||||||||| |||||  |||| |  ||| |    ||   | |||        ||| || |  |   | |     
gtaccttccctttctcagagcatttctttcttatttatctattgagtactatgtgcaaaaaagggggaaaaatggctagaagcttcttgcttgcccatcaaagcttatggagcctttttaagttttttgatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgcagACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGATTCTACTGGGGT--ACGCTTTGAAAAGGATTCATTTGG
















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|29680314|gb|CB676589.1|CB676589
EST:     TGCAATTGTAAGGGCTGACGCTGGATGGGCACATTGTGTTGCAATAACAG                         GTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAA
genomic: TGCAATTGTAAGGGCTGACGCTGGATGGGCACATTGTGTTGCAATAACAGgttgtgtatt ... actcaagcagGTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAA




















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), 64 (downstream exon)
Score: 23

GAAACTCCGGAGGCATTTCCTCTTCCTAGTGATATTGCAATTGTAAGGGCTGACGCTGGATGGGCACATTGTGTTGCAATAACAGgttgtgtatt ... actcaagcagGTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAAGGGTCATTGCAGACCATTCTGCAACTGGGGCTATGGATTGTGATAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtgaaaactgcacataactttgcattacactgattgaattccactcaagcagGTAAAGGTGATGTCTACACATGGGGTTGGAAAGAATGCGTTCCAACTGGAAGGGTCATTGCAGACCATTCTGCAACTGGGGCTATGGATTGTGATAAAAG
                              cactgat  putative branch site (score: 23)
                                         ttccactc  putative PPT
                ataacttt  TA-rich tract