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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG

Basic information

species Oryza sativa
transcript LOC_Os02g36740.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
tgattgaatctgttaa--ggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
   |  || |   ||      ||| | ||||    | |||||| |       |   |||   | | |||     ||||| | ||| | || |  | |  ||||| ||||| ||||||||||||||| ||||||||||||||||||| || | |||||||||||||||||| | |
--gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG

upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118957_T04 (Zea mays), 3'ss of exon 3
tgattgaatctgttaa--ggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
   |  ||    |||      ||| | |||||   | |||||        | |   |||   | | |||     ||||  | ||| | ||||  |||  ||||| ||||| || |||||||||||| | |||||||||||||||||||| |||||||||||||||||||| | |
--gtctaactgcttacctaagtttgtcttttgccatcctgtacgagccaagcattgcataaatctgtttgctaatttttttataccacatttgtttgcacagTATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAG

upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 1
tgattgaatctgttaaggattttttttttgttttactgtatttcttt---tgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
       |||| ||     ||||||||||  |||| | |  ||  ||   | |   |  ||| |  ||    | || | | | |     | |||   || ||||| ||||||||| | || || ||  | |||||||||||||||||||||||||  ||||| || || |||  |
--gagacatct-ttgttttttttttttttcctttaatatgcttgcttgcatttctattttgtgttaataatgatttgtggttttttggaaattttacgtacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAACTTGTGAGATATGTCACAAG

upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
-tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagat-tttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
 | ||      | ||   | |||||||||| ||||  | || |    ||| |  ||   | | | ||     ||  |||| |    ||  |||  ||  ||||| ||||||||| | || || ||  | |||||||||||||||||||||||||| ||||| || || ||   |
tttatgtggcatcttt--gttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG

upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
tgattgaatctgttaaggattttttttttgt-tttactgtatt--tcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
  |   |  |  | |  ||  |        | |||| ||| ||  |  |||| |  |  |  ||| |   ||| |     |   |||    | | |  | ||||  ||||||||  ||||||| ||| ||||||||||||||||||||||  |||  || || ||||| ||   |
acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctaga---ctagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG

upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 4
tg-attgaatctgttaag-gattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagat-tttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
|| ||||    | | |    |  |||  |     ||  | | ||||| |   ||  |||   | |   || | ||| | ||  ||   || ||| || | ||||| ||||||||  | ||||| ||| |||||||||||||||||||||||||||| ||||| ||||||||   |
tgtattgtcattatgagataaaatttagtactccttgatatttttctctctaactccat---tgtcagtcaaatttgttattgactgtatattttttttccagTATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG

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|29677125|gb|CB673400.1|CB673400
EST:     TAGCGGTAGCCTCAAG                         TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: TAGCGGTAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
EST: gi|27576199|gb|CA998893.1|CA998893
EST:     ACCTCGCCAAGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAG                         TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: ACCTCGCCAAGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
EST: gi|27578072|gb|CB000767.1|CB000767
EST:     AGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAG                         TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: AGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
EST: gi|29686717|gb|CB682992.1|CB682992
EST:     ACCTCGCCAAGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAG                         TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: ACCTCGCCAAGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
EST: gi|27554462|gb|CA998362.1|CA998362
EST:     ACCTCGCCAAGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAG                         TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: ACCTCGCCAAGAACCTCGAGAGCCCCTGCGCTTGTAGCGGTAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
                           ttttgat  putative branch site (score: 4)
                                          ttttatt  putative PPT
               tatatttctacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA