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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_Os02g06840.1
intron # 8
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttttctcatgccctcaaaatttgctaagttttgttaacccttgtctccagGGGTGTGAGATACTATGAACCTGAGCATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGAT
                                    tgttaac  putative branch site (score: 2)
                                          cccttgtctcc  CT-rich tract
                  tcaaaattt  TA-rich tract