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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG

Basic information

species Oryza sativa
transcript LOC_Os02g08120.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 5
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||||||||    ||       |  |        |||  |  ||| |  | | | |||| ||  |  |||||||   ||||||| ||||||||||| |||||| || | |||||||||||||||||||| ||||| ||||| |||||||| || ||||||||||| ||||||||| ||||
gtaagtcccaaaaaattgtttttgt--------atttctattgacacatatctaaactattccagattcatttacctagTGTACAAGAAGCACTATCCACCTACGCTAAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGAAAGGATGGCTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||||||||    ||       |  | || |    |    | ||| || | | | |||| ||| ||||||||||   ||||||| ||||||||||| |||||| |  |||||||||||||||||||||| ||||| |||||||||||||| || ||||||||||| ||||||||| ||||
gtaagtccc--aaaaatgtatttgtgtgctgtattctcacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||||||||    ||   | |    | |  |    | |  | ||| || | | | |||| ||| ||||||||||   ||||||| ||||||||||| |||||| |  |||||||||||||||||||||| ||||| |||||||||||||| || ||||||||||| ||||||||| ||||
gtaagtcccaaaaatgtatc--tgtgtactgtattcccacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||||||  ||  ||    |    || || ||    | |  |    |||  | | |      |  | || | | |  |||| || ||||| |||||||| ||||| ||||| ||||||||||||||  | || ||||| || |||||||| || || || || || || || ||||||||
gtaagt--tcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaatcg--tagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 6
-----------------------gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatt----tctattaactgtttgaatttca---tttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
                        ||  |  |||  |||| |  || | |     | | || ||   || |    ||| |||| | ||  | ||| |   |||  | ||| ||||||||||| || |||||||| ||||  ||||| || ||||| || || |||||||| |||||||| || || |||||||  ||||| |  || ||
gtagggttatgcttctacatcttttagtttttctctagcatcagtgctctccc-tgctcctacactgtaatagcatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCTGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTTCATAAGAAGCTGAATAGTGCAGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
|||||| |    || |  |  || |    | | || |||| |      | || | | |  ||  | || |||     ||| || |||||||||||||||||||| ||||| ||||||||||||||  | || ||||| || |||||||| || || || || || || || ||||| ||
gtaagtacat--aaacttcattgtttatgttctatccttctt-----ctgtaatga-tacttatacttgatt---gcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 4
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||||||  ||  ||    |    || || ||    | |  |    |||  | | |      |  | || | ||   |||| || ||||| |||||||| ||||| ||||| ||||||||||||||  | || ||||| || |||||||| || || || || || || || ||||||||
gtaagt--tcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaatta--tagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGTAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
-----------------------gtaagtcctctgaagcaaccatgatatgatacgatt--cttcatgatatt-tctattaactgtttgaatttca---tttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
                        ||  |  |||  |||| | ||  | |      ||   |    | |||   ||| |||| | ||  | ||| |   |||  | ||| ||||||||||| || ||||| || ||||  ||||| || ||||| || || |||||||| |||||||| || ||||||||||  ||||| || || ||
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagt---------cctctga-agcaaccat-gatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||||||         ||| ||| |  |  ||| ||| | ||  || ||||  |  |  || |    | |||||    ||  ||     |||||| ||||| || ||||||||||| ||| | ||||||||||||||||| |||||||| || ||||| ||  |||||||||||| ||| || ||||| ||
gtaagttcttgctttcctttgatattagtcattgatgt-atctgaatctttgtttttcttttgcctaatgttt----ttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagt-----cctctgaagcaaccatgatatgatacgattcttcatgatatttct----attaac-tgtt--tgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
||| ||     | | |   |    | |  |    |  | ||     |  | ||  |    || ||| ||||  || |||   | ||  ||||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| ||||| || || |||||  | || |||||||| || | |   || ||
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------gtaagtcc--tctgaagcaaccatgatatg--atacgattcttcat---gatatttctatt-aactgtttgaatttca----tttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAA-CAAAGCTGG
                                                                    || |||    | | | |||   |  | | |   |  || | || ||   |||     |||| ||   |||  | ||      || |   |||||| ||||||||||| |||||||| ||||| || ||||| ||| | || || ||||| |||||||| ||| | || || ||| | || || |||| |   
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttatctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA-

upper sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------gtaagtcctctgaagcaaccatgatatgatacgattcttcat--gatatttctattaactgtttgaatttca--------tttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
             ||||  |   ||  ||  || |      | | | ||| ||  |||    | | | || ||||   ||           || |   |||||| || ||||||||||||||||| ||||| || ||||| ||| | || || ||||| ||||| |||||  ||||||| ||| | || ||  ||||   
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

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|51946147|gb|CV152488.1|CV152488
EST:     GCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAAT                         TGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAG
genomic: GCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAATgtaagtcctc ... atttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAG
EST: gi|58613149|gb|CK040861.1|CK040861
EST:     CCGCGAGGCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAAT                         TGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAG
genomic: CCGCGAGGCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAATgtaagtcctc ... atttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAG
EST: gi|58695258|gb|CK083945.1|CK083945
EST:     CCGCGAGGCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAAT                         TGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGG
genomic: CCGCGAGGCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAATgtaagtcctc ... atttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 59 (downstream exon)
Score: 33

TTCCGACTTGGTTTGAAAATTTCCTCAGGATTTTGTGAGGGTATTCGCATCCGCGAGGCAAAAACTGAAGCTTTCATGGTTAAGGACCACAGAGGAGAATgtaagtcctc ... atttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
                          tattaac  putative branch site (score: 33)
                                         tttcattt  putative PPT
                atgatatttctattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG