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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttttggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtgacatgaatgagaatt...

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgat-gcttcctttcgagttgctattttac-----ctttttggcctgtatttttgtaacttatattgacttctcaat--gctgtgctgtgacatgaatg-agaatt-----------------------------------------------------------------
| | ||||| || ||  | || ||||| |||||||||||||||||||| |||||||| ||| | ||||| ||||| |||||||| || || ||||| |||||  ||  | ||  |||   ||   ||   |||      ||| | ||||   ||| ||  | | |  ||   ||||  |   | |   ||     ||  ||  |  |||                                                                 
ATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGGCTGgtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttccacag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcg----agttgctattttacctttttg---gcctgtatttttgtaactta--tattgacttctcaatgctgtgctgtgacatgaatgagaatt
| | ||||| || ||| | || ||||| |||||||||||||||||||| |||||||| ||| | ||||| ||||| |||||||| || || ||||| |||||  ||   ||  ||  |    ||||| |  |    ||||| |   |  |   |||||||   | |  ||  || ||     ||      |   | ||||         
ATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGACTGgtgagaattttatttcagtaatagttgttcatcagtcttttagaaagatttcttttttgtgcttaaaatacagattttattttgtaactttacaatatga---------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttttggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtg-acatgaatgagaatt----
||| |||||||| ||  | || |||||||| ||||| ||||||||||| || || ||||| || ||||| ||||| ||  | || ||||||||||| ||||||   |  | | ||||   ||     | |   | || |   |||  |  | | |||| | ||   |||||| |    ||      |  |   |  |  ||    
AATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctt--tttctcagtttattgacacctattttgctttgttttatag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttt-tggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtgacatgaatgagaatt--
|||||| ||||||||  | |||||||| || ||||||||||||||||| ||||| || ||||| |||||||| |||||||||||||| || ||| | |||||  ||||     ||||   |||  ||| |   |||| |    | | ||| | ||| | | ||  | || | |||  ||   || ||  ||    | |     
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttctt-ttgtcattatttattttattttttttctttctataagtaa-atcaa-ttgttaatattgaattgagaagtgtgatatatgcaa

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttttggcctgtatttttgtaacttatattgacttctcaatgctgtgc-tgtgacatgaatgagaatt---------
 || |||||||||||| | || |||||||| ||||| ||||||||||| ||||| || ||||| ||||| || || ||||| || || |||||||| |||||| |     |||||   ||||     ||  | | | |||    |  | |||    |   | | || | | ||||||     |||||   |    ||  ||         
TATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaag-----tccttctcagtt-----ttagcttatgtggaagtttctgttgattttagaaattaccttttaatgcttcatatgtgatgggggaaagccttttaaagttt

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgat------gcttcctttcgagttgctattttacctttttggcctgt-atttttgta-acttat--attgacttctca---atgctgtgc---tgtgacatgaatgagaatt-------------------------------
  | || ||||||||| | || ||||| || ||||||||||||||||| || ||||| ||||| |||||||| ||  | ||||||||||| || || || ||||| |       ||| | || |   |  | |||    |||    | ||| | | |  |  | ||||  || |||     |   | | | ||    ||  |  | | | ||| |                                
TTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGGGCGACTTgtatgttctcaggactttcctttggtgttttttttagggtttcaaacttgttagtatcatgtatttatttatggacagtataggcaggttttgtccatgcaatgtcattcagactctaagacatgcagttactctgtggttttgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttttggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtgacatgaatgagaatt---
  | || || |||||| | || ||||| ||||||||||||||||||||||| ||||| ||||| ||||| || ||  | || || ||||| ||||| || ||||| |  | |   | |   |  ||||  |   || | |  || | || |   | | |  ||   ||        | |    | |    | ||    ||   
TTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGGACGACTTgtatgtttttgcgccttgtactcttattagattattgttgtttgaacttctactagtcaattt---tttgaggcattttaagattattccagtggctgttcaa

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 13
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttttggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtgacatgaatgagaatt
  | ||||| || |||||||||||||||||||||||||||||||||||||| || || ||  | ||||| ||||| |||||||| || || || || || ||| |   ||   ||||   || |||||     |||     |                                                          
TCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGGTCGACTCgtaagtctctgattttc---tttctattcctaatttacaaacgccgcgcag-------------------------------------------------

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|58692820|gb|CK081507.1|CK081507
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58611693|gb|CK039405.1|CK039405
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58659487|gb|CK048167.1|CK048167
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCC
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCC
EST: gi|33804193|gb|CF327971.1|CF327971
EST:     CGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: CGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|66919084|gb|CX105932.1|CX105932
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGGGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58594482|gb|CF992790.1|CF992790
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttttggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtgacatgaatgagaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC