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

GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaaaccattctgggtctcatacactgttgttaattttgtgtgcttaaattggtttcaaacgtactccggtgctacatttttctgcatgtggtt...

Basic information

species Oryza sativa
transcript LOC_Os08g15040.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g15040.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G147726_T03 (Zea mays), 5'ss of exon 4
GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaaaccattctgggtctcatacactgttgttaattttgtgtgcttaaattggtttcaaacgta--ctccggtgctacatttttctgcatgtggtt-----
|||||||| || |||||||||||||||||||| ||||| ||||| |||||||||  ||||  ||     |||||||  || ||| ||| |||||    ||   |   | ||| |  ||  || |     || |||| |  ||||||         
GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaaacattt-----tctcata--ctattgctaaatttgtcattttccgtgattatcagaattaaacttcatgtttatatttcttagcatgtaagcacatg

upper sequence: LOC_Os08g15040.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G147726_T01 (Zea mays), 5'ss of exon 8
GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaaaccattctgggtctcatacactgttgttaattttgtgtgcttaaattggtttcaaacgta--ctccggtgctacatttttctgcatgtggtt------------------------------------------------------------------------------------
|||||||| || |||||||||||||||||||| ||||| ||||| |||||||||  ||||  ||     |||||||  || ||| ||| |||||    ||   |   | ||| |  ||  || |     || |||| |  ||||||                                                                                        
GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaaacattt-----tctcata--ctattgctaaatttgtcattttccgtgattatcagaattaaacttcatgtttatatttcttagcatgtaagcacatgaatattgacgtaggcatcagcagtcagcgcttcaatgcctaaaatgtcgatatttgtacttttttgaacgtaatggcag
















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:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|89162128|gb|CI103664.1|CI103664
EST:     TATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: TATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|86478438|gb|CI121071.1|CI121071
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|8956150|gb|BE229954.1|BE229954
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|86511016|gb|CI153649.1|CI153649
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|88906338|gb|CI375410.1|CI375410
EST:     GAGGATGAGCTAAAA-GTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|88239417|gb|CI240579.1|CI240579
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|86434337|gb|CI094680.1|CI094680
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|58666564|gb|CK055250.1|CK055250
EST:     GAGGATGAGCTAAAAGGTGCAGGCGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|86886528|gb|CI322760.1|CI322760
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTCCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|15850648|gb|BI798924.1|BI798924
EST:     GAGGATGAGCTAAAAGGTCCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|218486133|gb|FG956315.1|FG956315
EST:     GAGGATGAGCTAAAAGGTGCAGTCGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|87011925|gb|CI283812.1|CI283812
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
EST: gi|27554323|gb|CA998223.1|CA998223
EST:     GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAG                         GATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC
genomic: GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTC

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: 48 (upstream exon), 70 (downstream exon)
Score: 50

GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaa ... atgaatgcagGATCTTCCAGGTGCACTTGATGATGCTGCCATAACGGAATCATTAGAACTCCACAAGATTAAGAGCCGTCAATGGGCGATTTTCAAAACATCTGCCATAA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaaaccattctgggtctcatacactgttgttaattttgtgtgcttaaattggtttcaaacgtactccggtgctacatttttctgcatgtggtt

 AGGATG