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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcgcagtatggggtgatcttctgttttgattgattgtgtggatgtggattatagacagctaatccttagggttttttcgtgttttcttcaggagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC

Basic information

species Oryza sativa
transcript LOC_Os01g59600.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59600.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G445100_T01 (Zea mays), 3'ss of exon 1
------------------tgagcgcagtatggggtgatcttctgttt--tgattgatt--gtgtggatg-------tggattatagacagctaatccttag-ggttttttcgtgttttcttcag-gagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC
                  || | |   | ||   ||    | | |||  |||   |||  ||||| ||        |||  | | |  | ||  |    ||  ||  | || |  |     | | |   || | ||  | ||   ||||  |||||||||||||||||||| || |||||||| || ||||||||||||||                              
cctggtgggtttatattctgtg-gtgttttgtaatggcgatatatttactgacgaattttgtgtgaattgtttcactggggtcttggtatctcgtttgcagTAGTGGTCTCTTACTGGTGGCGGCGTAGAGGTGACGAAAAAACCTTGACAATGAGCAGCATAGGCACAGGTTATGATCTGTCTGTCACCACCTTCTCTCC------------------------------

upper sequence: LOC_Os01g59600.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 1
--------------------------tgagcgcagtatggggtgat---cttctgttttgattgattgtgtggatgtggattatagacagctaatccttagggttttttcgtgttttcttcaggagtagATAACACAGAATAG-TTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC
                          | |  | | |||  | | ||    || |||  || |  ||| ||||    |   || | || |  |  |  | |||  |  |        |   |  |   || | | | ||||||  ||||  |||||||||||||||||||| ||||||||||| || ||||||||||| || |                            
ttttttgtattaattttggtgttgtgtaatggtaatatatgattatatgtttatgtactggtgaattttgtgcggattagtt-ttgaaattttgttttcagGACTGATCTCCTCACTAGGCGCGTAGAGGTGA-AGAGAATAACTTGACAATGAGCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAG----------------------------
















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|88391292|gb|CI595546.1|CI595546
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|33692105|gb|CF320344.1|CF320344
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         ATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGT
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGT
EST: gi|33686423|gb|CF314662.1|CF314662
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|33686423|gb|CF314662.1|CF314662
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|88391006|gb|CI592914.1|CI592914
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|88391006|gb|CI592914.1|CI592914
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|218496122|gb|FG967266.1|FG967266
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88425566|gb|CI569290.1|CI569290
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88407414|gb|CI583872.1|CI583872
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88738269|gb|CI761777.1|CI761777
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88739654|gb|CI763162.1|CI763162
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88393093|gb|CI616577.1|CI616577
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAG                       
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT-A--AGgtatgcccta ... tcaggagt
EST: gi|88393093|gb|CI616577.1|CI616577
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAG                       
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT-A--AGgtatgcccta ... tcaggagt
EST: gi|88393093|gb|CI616577.1|CI616577
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAG                       
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT-A--AGgtatgcccta ... tcaggagt
EST: gi|88393093|gb|CI616577.1|CI616577
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAG                       
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT-A--AGgtatgcccta ... tcaggagt
EST: gi|58601557|gb|CK012085.1|CK012085
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|33657519|gb|CF280133.1|CF280133
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|12622988|gb|AU173201.1|AU173201
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88423678|gb|CI617030.1|CI617030
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|88423678|gb|CI617030.1|CI617030
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|88763617|gb|CI773064.1|CI773064
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88722486|gb|CI745996.1|CI745996
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88343491|gb|CI621859.1|CI621859
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|88343491|gb|CI621859.1|CI621859
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         G
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtag-
EST: gi|88300705|gb|CI589697.1|CI589697
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88420790|gb|CI564626.1|CI564626
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88454340|gb|CI569912.1|CI569912
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88718828|gb|CI742338.1|CI742338
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|29668731|gb|CB665006.1|CB665006
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|33686716|gb|CF314955.1|CF314955
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88396858|gb|CI578007.1|CI578007
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         ATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGT
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGT
EST: gi|88400550|gb|CI595971.1|CI595971
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|87008998|gb|CI304941.1|CI304941
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|163919763|gb|EG714885.1|EG714885
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg
EST: gi|88722475|gb|CI745985.1|CI745985
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGGAGTAG                    
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT----A--AGgtatgcccta ... tcagg

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: 72 (upstream exon), 50 (downstream exon)
Score: 6

GTCGGCACCGCCGCCGGAGCTCCTCCCTGCTCCCTCTACTGGGTTGGCGGGGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... tcaggagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggattatagacagctaatccttagggttttttcgtgttttcttcaggagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC
              agctaat  putative branch site (score: 6)
                             ttttttcgtgttttct  putative PPT
     attataga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcgcagtatggggtgatcttctgttttgattgattgtgtggatgtggattatagacagctaatccttagggttttttcgtgttttcttcaggagtagATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGC

- - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - -tgattgt
- - - - - - - - - - - - - - - - - - - - gtggatg