Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaatccaatatcctaatgattttaaggctatagcagtacacatgaattgatttcatttaggtgcatttgcttattggctgcttgccttcaactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG

Basic information

species Oryza sativa
transcript LOC_Os08g15040.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g15040.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 7
---ataaatccaatatcctaatgattttaaggctatagcagtacacatgaattgatttcatttaggt-gcatttgcttattggctgcttgccttcaactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
     || || | |  ||     |||  || |       ||||  ||||| |||   | |   | ||  ||||| || | | | |||  | ||| |  |||||||||||||| || |||||||||||||||||||| ||||| ||||| |||
attgaaagtctattcacccccaaattagaaaggc----tagtaagcatgagttgcccttaaaaatgttacatttactgaattgatgcacgtctttacatggcagGAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG
















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|86479923|gb|CI122556.1|CI122556
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|86478438|gb|CI121071.1|CI121071
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|8956150|gb|BE229954.1|BE229954
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|86511016|gb|CI153649.1|CI153649
EST:     ATACAGATAGGCTTGTAACGGCTAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|88906338|gb|CI375410.1|CI375410
EST:     GTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAA-GTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: GTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|88239417|gb|CI240579.1|CI240579
EST:     GAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: GAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|86434337|gb|CI094680.1|CI094680
EST:     GGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: GGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|58666564|gb|CK055250.1|CK055250
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGGCGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|88383993|gb|CI631883.1|CI631883
EST:     TACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTAATC-TTGAG                         GAGGATGAGCTAAAAGGTGCAG
genomic: TACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTA-TCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAG
EST: gi|86886528|gb|CI322760.1|CI322760
EST:     ATACAGATAGGCTT-TAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|15850648|gb|BI798924.1|BI798924
EST:     ATACAGATAGGCTTGTAAC-GC-AAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTCCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|218486133|gb|FG956315.1|FG956315
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTCGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|87011925|gb|CI283812.1|CI283812
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
EST: gi|27554323|gb|CA998223.1|CA998223
EST:     ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAG                         GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
genomic: ATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG

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: 64 (upstream exon), 48 (downstream exon)
Score: 49

ATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCATGCTATCCTTGAGgtatgggcca ... caactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgatttcatttaggtgcatttgcttattggctgcttgccttcaactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG
 aattgat  putative branch site (score: 49)
                                     cttgccttc  putative PPT
      atttcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaatccaatatcctaatgattttaaggctatagcagtacacatgaattgatttcatttaggtgcatttgcttattggctgcttgccttcaactggcagGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- -aatccaa
- - - - - - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgc