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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaagattcttgcattccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA

Basic information

species Oryza sativa
transcript LOC_Os08g38880.6
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G113726_T01 (Zea mays), 3'ss of exon 7
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaagattcttgcattccatgaggaaagaaagcctaatgttttattg-atttaatcttgccccttgtttta-taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
                                    || | | ||   |  || ||| ||  | | |  | |||    | ||       | |||||| | || | || ||||  |||||     ||||  | | |  || || ||   ||    ||| || ||    | ||| ||| ||||||| |    ||||||| ||||| |||||||| ||||||||||||| ||||||||| |||||||  ||||| |||||| |  | ||  ||||||||||||| 
-----------------------------------gta-agcctgcagtgcttgttgaat-tttcaattttctatctaaatctagctgctgaagtcaatgctca-tgttttgtcaaaga-----gcatgtcttaaataaggacaga--aacacattactgcatcctgtgttggcccctgttttaattttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG

upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G00740.3 (Glycine max), 3'ss of exon 8
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaa-gtcactactgaatgctttgctaaagat-tcttgcattccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
                                                                                | ||||    ||  |  | |  || |   | || ||   || ||||  | |     |   ||||||           |  |||||| |  | |   | | || | | |    ||||| || ||||||||||||||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| 
--------------------------------------------------------------------------------ttgccatgcacactgctagtgttggaaaatatgatattaatgtcttataataatacatagaagaaa-----------tgatgatttgaattggtttcct-ttctgtcc---acagCATACTTCATTGAGCCCGGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG

upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G12970.1 (Glycine max), 3'ss of exon 5
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacatt-caagtcactactgaatgctttgctaaagattcttgcat-tccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
                                                                                      ||||     |  || |||   |  |||  |||  |  ||  || || ||  | |||    | | ||||      | || | |  |||  |     ||| |  | ||||||| || ||||||||||| ||||| ||||| |||| ||||||||| ||| |||| |||||  |  | || ||| || |  ||||||| 
-----------------------------------------------------------------------------------gtgcattgtggatgcctgctgctagtgttggaaaatgtgattcaatgtctattggtaaat---gtcaaatg-----ataatgtgaatttgttctc---tttctgtc-tgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG

upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G12980.2 (Glycine max), 3'ss of exon 8
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacatt-caagtcactactgaatgctttgctaaagattcttgcat-tccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
                                                                                      ||||     |  || |||   |  |||  |||  |  ||  || || ||  | |||    | | ||||      | || | |  |||  |     ||| |  | ||||||| || ||||||||||| ||||| ||||| |||| ||||||||| ||| |||| |||||  |  | || ||| || |  ||||||| 
-----------------------------------------------------------------------------------gtgcattgtggatgcctgctgctagtgttggaaaatgtgattcaatgtctattggtaaat---gtcaaatg-----ataatatgaatttgttctc---tttctgtc-tgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAG

upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G02070.1 (Glycine max), 3'ss of exon 8
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacatt-caagtcactactgaatgctttgctaaagattcttgcat-tccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
                                                                                      ||||     |  || |||   |  |||  ||| ||  ||  || || ||  | |||  |     |   |  |||  ||||  |||  |    ||| |        |||||| || ||||||||||| ||||| |||||  ||||| ||||||| ||||||||  ||||  |  | || ||| || |  ||||||| 
-------------------------------------------------------------------------------------gcattgtggatgcctgctgctagtgttggaaaatatgattcaatgtctattggtaaatgacataaaggataatatgaatttgttct--ctttctgtct--------gcagCATACTTCATTGAGCCCTGATGGAAAACTACTTGCTGTTGTTGGAGACAACCCAAAAGGGTTACTGGTGGATTCTCAAACAGGAAAG

upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G40060.1 (Glycine max), 3'ss of exon 8
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaa-gattcttgcattccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
                                                                                      ||||    |    ||| | || |     | | |||  |    |   || |  | | | |    || |   |  |||||| |  | |   | | || | | |   ||||||||| ||||||||||| ||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| 
--------------------------------------------------------------------------------------cattgctttgcacacttagtgttggaaaatatgatattaatgtcgtataataatacata----aaagaaatgatgatttgaattggtttcct-ttctgtcc---gcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG

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|38477499|gb|CF961632.1|CF961632
EST:     TGGAAAAATTTCAAATTTGCAATAATTGGCGTTTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCTGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|29640281|gb|CB645290.1|CB645290
EST:     TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|88267006|gb|CI378941.1|CI378941
EST:     TTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|29677554|gb|CB673829.1|CB673829
EST:     TTTCAAATTTGCAATAATTTCCGTTTTCCTGGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|88271495|gb|CI387548.1|CI387548
EST:     TTCCCTTTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|29669309|gb|CB665584.1|CB665584
EST:     TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|29640492|gb|CB645501.1|CB645501
EST:     TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
EST: gi|88271367|gb|CI387420.1|CI387420
EST:     TAATTTCCCTTTTCCTTGGGCTG-TAAT                         CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC
genomic: TAATTTCCGTTTTCCTTGGGCTGTTAATgtaagccttt ... taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
         taatgttttattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaagattcttgcattccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG