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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

Basic information

species Oryza sativa
transcript LOC_Os02g13110.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
gtgaagtttcgta--acctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
||||| |||| ||  | ||||||||     |||  | |  | | || |  ||    ||||| ||  ||||    |  |||||||||||||| |||||| |||| || || |||||||| |||||||||||||| || || || || || |||||||| | |||||||||||| ||||| ||
gtgaattttcttatcatctgaatgagaatgaaagagccg-tatcaatatctgctgtaatctgatagcgtg--ggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
gtgaagtttcg----taacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
|| |  || |     | |  | | | |||   ||    |   || |  |   | |||     || |  |  | | ||||  | ||   ||||| |||||| ||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||| | |||||| ||||||| ||||||||
gttagattcccatgtttatataagtaatgagcaatgaattcctgct--gctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
gtgaagtttcgtaacc--tgaatgatggcaaaaatgtcaatgttaagac-atgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
     ||||  |||    ||||| |||       |   | ||||  | |   || | ||     |    | ||  ||| | | |   ||||| |||||| ||||||||||||||||||| || || || || ||||||||||| ||||| |||||| | || || |||||||| ||||||||
-----gtttgataagtgatgaattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgc-cagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
---------gtgaagtttcgtaacc--tgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
          ||   ||   |||    ||||| |||      ||   | || |  | |  || | || ||  |    | |||  ||      |  ||||| || ||| ||||||||||||| ||||| ||||| || || ||||||||||| ||||| |||||| | ||  | |||||||| ||||||||
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataa-ctggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
|| |  || |      || ||||  ||||  |  |   || |  |   | |||   | || |  |  | |  |||  | ||   ||||| |||||| ||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||| | |||||| ||||||||||||||||
gttagattcccatgtttggatga--gcaatga-atttctgct--gctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatt-tcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
|| | ||||| |||     ||  ||  | | ||     ||   ||      |       ||||   |     || |  || ||| |||||||||||| |||||||||||||||| || |||||||| || || |||||| | |||||  ||||  | || |  || || || ||||||||
gtca-gtttcctaat----attttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gtga-agtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
|||| || ||| |   |||    ||     |  |||  ||  |      |||   || ||||   |||  |  |||   |  |||||||| || ||||||||||||||||| || || ||||| |||||||| |||||||||||||| |||||| |  | || ||||| || ||||||||
gtgagagcttctt--tctgtggcatcttttatttgttgattctg-----tgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------gtgaagtttcgtaacctgaatgatggcaa---aaatgtcaatgttaagacatgtca-caatctaat-gccgt-gttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
                                 |   ||    | |  ||||||  |  |         | | ||| ||   || | | | || ||||     |  ||| ||  |||||   ||||| |||||| |||||||||||||||| || || ||||||||||| |||||||||||||| |||||||| || || || ||||| || |||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gtgaagtttcgtaacctgaatga---tggcaaa----aatgtcaatgttaagacatg--tcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
||||  || | |  |    |  |   |  || |    ||  || |  |||     ||  |   ||| | |  |  ||||  |||| |  | | ||| | |||||| ||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||| | ||||| || || || ||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------gtgaagtttcgtaacctgaatgat-ggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
                                   |   |  |  | |||||  || || |    || |||  ||  |   |    | |  ||     | | ||| | | | |||||   ||| | || ||| | ||||||||||||||||| |||||||| ||||| |||||||||||||| ||||||  ||| ||||||||||| || |||||
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgt--atcattttatccataatgatggtgggacttgt-actctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcat--cttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
            |    ||    ||    |||| |  | | | ||   || |  ||       ||| |    | ||   || |||| ||  ||||| ||||| |||||||| || || || || || || || ||||| ||||| |||||||| ||||| |||||    |||||||||||||| ||||||||
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
-------gtgaagtttcgtaacctgaatgatggcaaaaat-gtcaatg--ttaagacatgtcacaatctaa--tgccgtgttaattt-catcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
        | | || | |  |   |  | ||   |  | | |||| |      ||   | ||   ||  ||  ||  |     |||  | |||||||||||| |||||||| ||||| || || || || || ||||| |||||||||||||| |||||||||||  | ||||| |||||||| || |||||
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
------gtgaagttt---cgtaacctgaatgatggcaaaaat-gtcaatgttaagacatgtcacaatctaatgccgtg--ttaatttcatctttt-gcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
         || | |    | |  | |||    || |  | | |   |||||        |   | |  | |  |     ||| || | | |||| ||||||||||||||| ||||| || |||||||| || || || ||||| |||||| | ||||| |||||  | ||||| |||||||| || |||||
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

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|58663865|gb|CK052551.1|CK052551
EST:     ATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGAACTAAG                         CTCTGTGATCTATATGAAAATGATT
genomic: ATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAGgtgaagtttc ... tcttttgcagCTCTGTGATCTATATGAAAATGATT




















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: 53 (upstream exon), 67 (downstream exon)
Score: 6

TTATGGGATATAAACATGGATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAGgtgaagtttc ... tcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
                                  tgttaat  putative branch site (score: 6)
                                        tttcatctttt  CT-rich tract
                                    ttaatttcatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA