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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag

Basic information

species Oryza sativa
transcript LOC_Os01g70960.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA16G06700.2 (Glycine max), 5'ss of exon 6
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagct--cctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag
||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| ||||| ||||||||||| ||||||       || || ||            |  | |    ||  | ||  || | |||   |   |  ||    | | | |    ||||   ||| ||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTCCTGCTACAGAAGCTCAGgtattaaatttgcttctggaggaatatggtttagtaaatcttcttaaaaatgggatttgatag-aatctagctcattttctcttaatgtttgttgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 6
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgta--gctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag
||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| || || ||||||||||| ||||||       ||||| ||        |     |  | | | |    ||  |     ||   |   | |||    | | | ||   ||||   ||| ||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCCCTGCTACAGAAGCTCAGgtattatatttgtttctggaggaatggtttagtaaatcttcttacaaa--tagaaattggaaaaaatgtagctcattttattttaatgtttgttgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 5
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtag---ctcctgtttttgag----ttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagta-ttagactattttcatatgtaaattgtag----------------
 |||||||| || ||||||||||| || || || ||||| || ||||| |  |||| ||| || || ||||||||||| ||||| || |||||||| |||||      |||| |  || ||    |  | ||||  |   |  ||||  | |   |     ||  | ||||   | ||| |  || || |  | |   || |                  
CTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTCCTGCAACAGAAGCACAGgttagttttcctctgcttaagaaaataatttgcagaccataaagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 6
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctgtttttgagttgtctgcactctg--caccgtttagtta-agctgtggtttatc------actgaagtattagactattttcatatgtaaattgtag
 |||||||| ||||||||||| ||||| || || ||||| || ||||| |||||||| ||| | |||||||||||||| || || || ||||| || ||||| | |  |   | |    |   ||||   ||    |   |||  |  |  ||    || |         |  |  |||       || ||||  |    || ||
CTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggtttt-catctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcag

upper sequence: LOC_Os01g70960.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagc-tcctgtttttgagttgt-ctgcactctgcaccgtt--tagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag
 || ||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| || || |||||||||||||| || || || |||||||| || ||| | ||||||  ||    |||  |  | | ||||   ||  || | ||| | |||   |  |||||  |  |     || || |  |    |  |   
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatgg--aaaaactgatattct----catcttaacgttggcacag---

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|86486845|gb|CI129478.1|CI129478
EST:     ATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: ATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|89168991|gb|CI020531.1|CI020531
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|27920999|gb|CB096807.1|CB096807
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|88222829|gb|CI220894.1|CI220894
EST:     TGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86502387|gb|CI145020.1|CI145020
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86433950|gb|CI094293.1|CI094293
EST:     ACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: ACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86508914|gb|CI151547.1|CI151547
EST:     GCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: GCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|86418967|gb|CI053768.1|CI053768
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
EST: gi|87029581|gb|CI257376.1|CI257376
EST:     TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAG                         ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG
genomic: TTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctg ... taaattgtagATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTCCAGCTACAGAAGCCCAGgtagctcctgtttttgagttgtctgcactctgcaccgtttagttaagctgtggtttatcactgaagtattagactattttcatatgtaaattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC