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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA

Basic information

species Oryza sativa
transcript LOC_Os02g50320.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G832989_T02 (Zea mays), 3'ss of exon 9
-----------gtatggcactagaatt--cctgtttattatggatttaatgggaccaatgctgtgggtc-atgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
           |||| | | |||| |   | |  |   ||| |  |    || | ||   |||||| || |||  || ||| |    || |||  |||||||| | ||||| || ||||||||||||   || || | |||||||||||||||||||| ||||| |||| |||||||| |||||||  || |||| ||  
gttcaaaactagtattgaattagattggacatagtggatattgtatgtgaggaaacatgactgtggttctatggtttagcttatcaactgttgcctacagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCTAAAAAGAAGAGGCAAGAGATAGCTGCTTTGGAGAAAAAATTTGCCGCGG

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatg-cctttgctaactgcctc--------ttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
|| | | | |  | ||  | ||   |||  || | |     | |||  ||    | ||   ||| ||||||||   |        || | |  |||||| ||||||| || ||||||||||| ||||| || |||||||| ||||| || ||||||||  |||| |||||| | ||||||||||| || ||||| |
gt-tagtattt-atttgtttttggatattaatcttagatttctaat--tgataattataatcttagctaactgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
gtatggcactagaattcctgtttattatggatttaatgg--gaccaatgctgtg--ggtcat-gcctttgctaactgcctc---------ttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
||| |    | |  |   | ||   | ||||| ||||    |||   |  |||     | || | | ||||||| ||  ||         |  | || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||||| || ||||||||  | || |||||||||||||||||||| || |||||||
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
gtatggcactagaattcctgtttattatggatttaat----gggaccaatgctgtgggtcat-gcctttgctaactgcctc---------ttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
|||      | |  |   | ||   | ||||| ||||    |    |     | |   | || | | ||||||| ||  ||         |  | || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||||| || ||||||||  | || |||||||||||||||||||| || |||||||
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
----gtatggcactagaattcc-tgtttattatggattt---aatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
    ||||     |    ||   | || ||  | |||||   | ||  |   ||  | |  |  |     ||||  | ||  | || | |  |||||| ||||||| || ||||||||||| ||||| || |||||||| ||||| || ||||||||  |||| |||||| | ||||||||||| || ||||| |
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagcta-attgttgc--aatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------gtatggcactagaattcctgtttattatggatttaatgggaccaat---gctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
                     ||   |       || ||   ||| | | | || ||   || || |   | |||       |    |  | |     |  ||||   ||||| | || || ||||| || |||||||| ||||| ||||| || || || || |||||||| || || |||||||| ||||| || ||||||||||| |
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
--------gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaac-tgcctcttgtttac--agATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
        || |    |     ||||||||  ||   |  || ||  ||  |||| |||     ||   | |    |  ||  |  ||| ||   |||||||||| || ||||| || |||||||| ||||| ||||| || ||||| || |||||| |  |||| |||||||  |||| ||| ||||||||||| |
gtttgctagtgtttggccttttttcctgttctttgccgcctttatatga--aatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
---gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
     ||  | ||  |  | |  | ||  |||   ||||   |||   || |     |       ||| ||      | ||  ||  ||||||| ||||||||||| || || ||||| ||||| |||||||| || || || ||||||||  | || || ||||| |||||||| || |||||||| |
gtaaaatctctctgaatgtaccatataaaatgttgttaaaaagac--gtgtttgtaatggaagtcttgata------tttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA

upper sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
|| ||| | |    | |   | | |  |    |   |   |   ||  | | | |||||  ||||     ||    |  ||| |||||| | || || ||||||||||||||||||||||| |||||||| |||||||| ||||||||  | || || ||||| ||||||||||| || ||||| |
gt-tggtattcttgtcctcatctgtcttatgat-gctttaattcatatttttgctcatgtatttg---gatgtaattctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA

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|218485743|gb|FG955661.1|FG955661
EST:     TGCCATGAGAAAGATCAAAGTCTAAAAGACAAGGATGATGCAATTGAG                         ATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCT
genomic: TGCCATGAGAAAGATCAAAGTCTAAAAGACAAGGATGATGCAATTGAGgtatggcact ... ttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCT
EST: gi|58684724|gb|CK073411.1|CK073411
EST:     CATGCCATGAGAAAGATCAAAGTCTAAAAGACAAGGATGATGCAATTGAG                         ATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCT
genomic: CATGCCATGAGAAAGATCAAAGTCTAAAAGACAAGGATGATGCAATTGAGgtatggcact ... ttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
                                tgctaac  putative branch site (score: 1)
                                         cctcttgttt  putative PPT
                                             ttgttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT