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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcatcacatggttttaactgttctttctgacaatgtctcctttccttttctcatgccctcaaaatttgctaagttttgttaacccttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT

Basic information

species Oryza sativa
transcript LOC_Os02g06840.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 7
gtaagtgcatcacatggttttaa-ctgttctttctgacaatgtctcctttccttttctcatgccctcaaaatttgctaagttttgttaacccttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT
|||||   |||   |||    |  |      |  |||  ||      ||| ||      | |   |  | |  || |     ||     ||||   ||||||||| |||||||| |||||||| ||||| ||||| || |||||| | || ||||| || || ||||||||||| |||||||| |||||| ||||||| || 
gtaagcttatcttgtgggcagagtccaggtctcttgaggatagtaattttgct----gaaagttgttgacacatgtttgtgctt-----ccctccactccagGGGCGTGAGATATTATGAACCCGAGCACTGGAAGTTCGGCGAATCGGGGAACAAGTACTTCCGGCATGCTACCGGTCAATTATATGCTGTTTCAAAGGAC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgcatcacatggttttaactgttctttctgacaatgtctcctttccttttctcatgccctcaaaatttgctaagttttgttaacccttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT
    ||    |||||  || ||| | |||         || | ||   |   ||||    |     ||||| |      || |     ||||| |   |||||| || |||||| ||||||||||  | ||||||||||| ||    || ||||| ||||| || ||||||||||| ||  | ||||||||||||||||||
----gtaagacacattcttataattcttc---------atctttcagatagatttcaagagattctaaaatgtttctgtttct-----cccttatgaacagGGGAGTCAGATACCATGAACCTGAATACTGGAAATTTGGTGAGGAGGGTAACAAGTATTTCCGTCATGCTACTGGGCAGCTATATGCTATTTCAAAAGAT

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgcatcacatggttttaactgttctttctgacaatgtctcctttcctttt--ctcatgccctcaaaatttgctaagttttgttaacccttgtctc-cagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT
                    ||| ||   ||  | | | ||| |   || | |    ||  |    ||  | |||  ||   |||||  |   || | |  |||||| ||||||||| ||||||| ||| ||||||||||||| ||  |||||||||||||||| || || ||||| || ||  | ||||| ||||||||||||
-------------------gtaagtgactttctttagattgttttggttacgtgaaactgtttagttcttagtttctta---tttgtccatatttttgtaacagGGGAGTGAGATACCATGAACCCGAGTATTGGAAATTTGGTGAGGCAGGAAACAAATATTTCCGTCACGCTACAGGACAGCTATATGCCATTTCAAAAGAT

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|29682551|gb|CB678826.1|CB678826
EST:     CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGATCCTGAGCATTGGAAATTTGGCGATCCAGGAAA
genomic: CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
EST: gi|2799316|gb|AA752305.1|AA752305
EST:     CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTTGGCGATCCAGGAA
genomic: CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTT-GGCGAACCAGGAA
EST: gi|86868611|gb|CI332988.1|CI332988
EST:     CAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
genomic: CAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
EST: gi|2799246|gb|AA753771.1|AA753771
EST:     CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTTGGCGAACCAGGAA
genomic: CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTT-GGCGAACCAGGAA
EST: gi|88274436|gb|CI394842.1|CI394842
EST:     CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
genomic: CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
EST: gi|29657303|gb|CB653578.1|CB653578
EST:     CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
genomic: CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
EST: gi|87006638|gb|CI295021.1|CI295021
EST:     CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA                         GGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA
genomic: CCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAA

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: 74 (upstream exon), 63 (downstream exon)
Score: 43

CAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAAgtaagtgcat ... ttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttttctcatgccctcaaaatttgctaagttttgttaacccttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT
                                    tgttaac  putative branch site (score: 43)
                                          cccttgtctcc  CT-rich tract
                  tcaaaattt  TA-rich tract