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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaatggaaaccttatgtgattgatactggttgcaaaaattgagcacataacccatctcaataagatttaacattccctaatcagaattgcggatgttcttttgtaatgctgtttgtacctaatatcattgtaaaatgtgagttcacaagtgctcatgctaccatttacaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcaatggaaaccttatgtgattgatactggttgcaaaaattgagcacataacccatctcaataagatttaacattccctaatcagaattgcggatgttcttttgtaatgctgtttg-tacctaatatcattgtaaaatgtgagttcacaagtgctcatgctaccatttacaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG
                                                                                                          ||     |||||   ||  ||  ||| || ||   |   |  ||  ||     |||  || ||| |   ||||||||||| | |||||| ||  | |    ||| ||||||||||| |||||||||||||||||  |||||||
---------------------------------------------------------------------------------------------------------gtgagtatctgttaaatatttacaatcgttttatttttcaaaatcttaa-----cata-tatcatct---atttcagCATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 8
gtatgcaatggaaaccttatgtgattgatactggttgcaaaaattgagcacataacccatctcaataagatttaacattccctaatcagaattgcggatgttcttttgtaatgctgtttgtacctaatatcattgtaaaatgtgagttcacaagtgctcatgctaccatttacaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG
                                                                             || | |  |     ||||   || | ||    | |   |     |     |   ||||| |    | |  |  | |||||   |   ||  |||    ||||||| ||||||||||| || ||  ||  ||| || ||||||||||||||||| ||||| |||||||| ||
-----------------------------------------------------------------------------ttacatttttgtctttgcctctgatattaaacattatagagcaaatgcttttctattgttagtattta--ttgccagtgcaattaacacattttt--gtttcagCCTCTAAATGGAAAGACACCACATCTGGTCAACATGTTGATTATGATCAGAGGCCTGACATATTCAG
















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|29629024|gb|CB634035.1|CB634035
EST:     ACCTGGATCACCTGATGAGAAGAAACNNNNNNNGATTGATCTTGGCTTAG                         CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAA
genomic: ACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAGgtatgcaatg ... acaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAA
EST: gi|29623307|gb|CB628318.1|CB628318
EST:     ACCTGGATCACCTGATGAGAAGAAACNNNNNNNGATTGATCTTGGCTTAG                         CATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAA
genomic: ACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAGgtatgcaatg ... acaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcattgtaaaatgtgagttcacaagtgctcatgctaccatttacaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG
 acctaat  putative branch site (score: 3)
                                         atttacaattt  TA-rich tract