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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaattgccttccttgtctttcttttcaaggaaaaaagggaaacaacactggcttcattttaattttattgcaaacaatccctgaaacttgttctaaacaaacattagtccttttcctcatagaccactttcatatttctgtacaatgcatttttttcatagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g67220.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 3
gtagcaattgccttccttgtctttcttttcaaggaaaaaagggaaacaacactggcttcattttaattttattgcaaacaatccctgaaacttgttctaaacaaacattagtccttttcctcatagaccactttcatatttctgtacaatgcatttttttcatagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG
                                                      |  |  | | |   ||  | || |  |     ||||     ||  |||||| |  ||  |      |    |  ||| |||   ||  ||   |  |  |   | |||  ||   | ||     ||| ||  || |  |||| |||||||||||||| |||||||| ||| | |||||  | || || |||||||||||||||||| | || ||||||||||
------------------------------------------------------gtattgtct-accattcctacagatga-----gaaaaagaatc--aacaaaaaa-agagcggcgggtggaggggcacattc---ttcttggtaatagggtaactatcaacgaattgaaa-----tgtttgctataaactttt-cagGAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG

upper sequence: LOC_Os01g67220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AC155376.2_FGT005 (Zea mays), 3'ss of exon 3
gtagcaattgccttccttgtctttcttttcaaggaaaaaagggaaacaacactggcttcattttaattttattgcaaacaatccctgaaacttgttctaaacaaacattagtccttttcctcatagaccactttcatatttctgtacaatgcatttttttc----atagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG
                ||||||  | || | |  ||| ||  | ||| | |        |     |        | | |  | | | | |     | | ||  |||     |  || ||       || |  || || |   |||||| |||||| |||      | | |  |  || ||||||| ||  ||    ||||||||||||||||||| |||||||| ||| | |||||  | || || |||||||||||||||||| |||| ||||||||||
-------------gtattgtctagcattcctataaaagaaaaggaaccataaaaaaaagagggggaggggggctccatc--ttcttaacaacgaatgtgaa--aactgccatttttctctgttcctacaatgttaatttggttgtacattgcattgtttctcaggaaaaaaaaacaatttcttgtttgaaata---tttttcagGAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCACGTATATTTCCTG
















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|88575864|gb|CI670009.1|CI670009
EST:     AGATGGGAGCAGTGGAGAAGTTGCACGTTGATCATTACCATCGATACAAG                         GAAGACATTGAACTCATGGCCAGTTTGGGTTCCCGTGCTTATAGATCTTCT
genomic: AGATGGGAGCAGTGGAGAAGTTGCA-GTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
EST: gi|88356318|gb|CI652755.1|CI652755
EST:     TAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAG                         GAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
genomic: TAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
EST: gi|88761211|gb|CI770767.1|CI770767
EST:     TACATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAG                         GAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
genomic: TAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT

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: 59 (upstream exon), 70 (downstream exon)
Score: 34

AACGTATCTTAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatgcatttttttcatagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG
                      cagtaac  putative branch site (score: 34)
                                              ttttttc  putative PPT
       atttttttcataga  TA-rich tract