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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG

Basic information

species Oryza sativa
transcript LOC_Os03g14260.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaat--acctgtatacact---------aaatgcatgttttccttggtcatttttc----tttgctgcccatttgatttctgcaactacattattttactg-atttgtctcat--gtcaattatttatctagaa---tattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
|||||| ||  |||||||  ||||| ||||    ||   | ||  || ||          | || | ||||||  ||   |||||||     ||||||  | || | ||||  |    |  | ||| || |   ||||   | ||  || |||  |||| |||  |   | |||| || |  || |||||| ||||| |||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||| || |||||||||||||||||||||
gtaagttat--tagatgttgagatgtatagtggtatcggcttggctagaccgctagattaagattcttgttttatttcaacattttttctgttttgctaacaatat-atttagggtcttgtagtatgtttcgacatttaatttatcagttaatgttttaactatgacttttttttttggaacaaccagGTCTGTATTTTATCCAGCCACAGATGTAGTTGTTTTGAAGTTCATGGTTGAGGTTTGCTGGGCTCCTATGCTTGCAGCATTCAGTGTTCCACTTGACCAG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
                                                           |||  |   || ||||  |||  |  |  |||| |||     |  ||||| ||     ||    ||| | ||   ||||| || |  | | | ||   | |     |||||||| |  ||| ||||||| ||||| ||| |  | | ||||||| | ||||| |||||||| || ||| | ||||||||||||||||| ||||| || 
-----------------------------------------------------------ttttatacttctttttctttttattactgtttgtttt-----aaaacatt-ttggggggaaagttcttaagtgtgttattgatatttattttcttgcaatttg--tagGTCAGTCTATTATGCAGCAACTGATGTTGTAATCCTCAGATTCATGATTGAGGTGTGCTGGGCACCAATGTTAGCTGCCTTCAGTGTTCCTCTTGATCAA

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttct------ttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaa-------tcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
                         |  || ||| |  || | |||    |    |||||         ||||| |||      ||  |   ||||| |  || | ||||||  |  |  |||| ||  |||| ||  ||   |||| ||     | | | |||||  |       ||||||||   | |||| | || |||||||| ||  || | | ||| ||| | |||| ||| |||||||||||||||||||| |||||||| || || ||||||
-------------------------gtaagatcactctctct-tacttgcatcatatgttgataacaaccatttctctgtagacttagtattcatttcaactcag-aactactctcctgaactgtttcatctcttgggaaacttttagctgatgcagtatttgaattgactcgttttcagGTCAACCTACTATGCTGCTACAGATGTGGTTATTCTCAGATTTATGATTGAGGCTTGTTGGGCTCCTATGCTTGCTGCATTCAGTGTGCCGCTAGACCAG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
                                                                 |  |   |||| |||  |    ||||   |        || | | ||  |||   |       ||| |  | ||  | |   || |||  |         |||||||| |  ||| ||||  | |||||  |  |  | | ||| ||||| |||||||| |||||||||||| | || || |||||||||||||||||||||
-----------------------------------------------------------------ttctttcttttttttaattttaatttagctatgatttttatact-ttcaactacctgaaaaagtgt-atctcttggtttctgatttttgttttccactgtagGTCAGTTTATTATGCAGCCTCGGATGTGATTATACTCAGATTTATGGTTGAGGTTTGTTGGGCTCCTATGTTGGCAGCTTTCAGTGTTCCACTTGACCAG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
                                             |  |   |  |  |   |   | | | || | | ||||| |  | |||     |||||       ||||   |||||   ||  |    ||| ||   | | | | ||| |         |||||||| |  ||| | ||||||||||||||  |  | | ||||||| | || || ||||||||||| ||| | ||||||||||||||||| |||||||| 
---------------------------------------------cttttgttttacatgccctaagttgagttgtgtatgctggctgtgtga-----gcaacc------ttttg--gattttcttctcgatgtttacttgctttggaaaatttgt---------agGTCAGTTTATTATGCTGCAACAGATGTAGTGATCCTTAGATTCATGATTGAAGTATGCTGGGCTCCCATGTTGGCTGCCTTCAGTGTTCCGCTTGACCAA

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ15473 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaat---cagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
                                                                                                                           | || | |   |||| | |||   |  || | |||| |      ||| || || |  ||  || |  | ||||| |   | || |    ||||||||| |||   |||||||| |||||||| ||||||||||||||||| ||  ||
------------------------------------------------------------------------------------------------------------------gtaagagcatttc-tatttcttatatttctgagaacttatttgaacgttcttgcagCTCTGTCTATTACTCACCGTCTGATGTCGAGATCTTAAGGCCCATGGTCGAAGTTACATGGGCTCCAATGCTTGCAGCCTTCAGTGTTCCACTGGAGAAG

upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
                                                                                                  | ||   | ||  |||     ||  | |  |    |  | |||| |  | | | ||          ||| || || |  ||  || |  | ||||| |   | || |    ||||||||| |||   |||||||| |||||||| ||||||||||||||||| ||  ||
--------------------------------------------------------------------------------------------------gtaagagcttttcttt-----ttcttatatttctgagaacttatttgaactttcttg---------cagCTCTGTCTATTACTCACCGTCTGATGTGGAGATCTTAAGGCCCATGGTCGAAGTTACATGGGCTCCAATGCTTGCAGCCTTCAGTGTTCCACTGGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
 tactgat  putative branch site (score: 2)
                  tcaattatttatctag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttctttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaatcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC