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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt...

Basic information

species Oryza sativa
transcript LOC_Os02g07870.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 8
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt---------
      ||||| ||||| ||||| || ||||||||||||||  |||||||||||||||| || |||||||| |||||||||||||| |||||||||||||||||   | | |||| | ||||  |||   || ||  | | |  |||   | ||||||     ||| ||   | ||| ||  | | ||||      | |          
TTGCCTGATGGCCGTGAGGAGTCAGTCATGAAGAGAACAACCTTGGTGGCTAACACATCAAATATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaaaactctgttgc-cttgat--att-taacctttggtcgtg-tagccacagatatc----aagtctgaaactcttagtgctgtggtaggaaacatatcaatatcaga

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 11
----------------ACAGAG---GATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt
                |||  |   ||||| ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || |||||     | || | | ||||  |||    || |  |||||  |||   | ||| |       |         || ||  |   |  |           
TCCCCAGTTGACGATGACATTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTgaagcttccatttacactggtaaaaccctgttac-cttgat--att----cacttggccatg-tagccacagatgtaagccctgaaactagtgctgtggtagggaaca-----------

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctg-attgattgctacattaagccataatagtg---tctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt
      ||||| ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || |||||     | || |      ||| | |    |||  ||||| |   ||     |||| |    |   |||      |   | ||| ||| |||   | ||   
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatca-atattagaaatatt---

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtc-tgatatccatatagtgtgccccacttt--gtcatatagtagttgttttgtt
  |   ||||| |||||||| ||||| |||||| | |||||||| ||||||||||| || |||||||| || ||||||||||||||||| |||||||||||| |   |||||  ||    |||    | ||  |  |   ||  | | |   | ||||  |   | | |  || | |     |  ||   || |||  |||  
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttg-aattctaggatatctctatttattgttgagaaataatatttactaactctttcctattgccaattgtaatttaattggcttg--

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt
  |   ||||| |||||||| ||||| |||||| | |||||||| ||||||||||| || |||||||| || ||||||||||||||||| |||||||||||| |   ||||   ||     |  |||  |  |||       | || | | |  ||    | | || |   | ||| |    |||     ||||     |
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGCACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtagctcttgaattctatttatttattgttaagaattaatatttactaattctttcgtattgtcaactgtaatttatttggcttgtgaaagt

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt
      ||||| ||||| || ||||| |||||  | || ||||| || |||||||| || ||||||||||| |||||||||||||| || ||||| |||||||||| |      | |    || || | ||  || |   ||   | || || ||   ||| |  | |       |||    |  | |    |       
TTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttcaggcacacagatttaatagtta--ttgatgaatcccattgcct-atgctcattttttttttttttttttaatgtg-aattccag-------

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccac-tttgtcatatagtagttg-ttttgtt-----
      |||||  | ||||| ||||| ||||||||||| || || || |||||||| || ||||||||||| |||||  | || ||||| |||||||||||||||| |   ||| ||    || |||| |   ||| |   |   | | | |  |||   ||   | | |||  | ||| |   ||||   |    ||||||     
CTGCCTGATGGGAGAGAAGAATCTGTCATGAAGAGAACTACGCTCGTAGCTAACACTTCTAACATGCCTGTGGCTGCAAGGGAGGCTTCAATTTATACAGgtaatgct---ttgatc----ttcattgttttgttatgaattgggattcttttgtatgtgtagtttctacccttcatttttttcatagggctaaactttgtttgagc

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt--
      ||||| |||||||| ||||| |||||| |||| ||||| ||||| ||||| || || |||||||| ||||||||||| ||||| ||||||||||||||   | | || || || ||| ||| |||    | |  ||    | ||   | |    |  |||       |  ||    | | | | || || |||   
CTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatat-ttacttct-attcattactagcacatgaaatggctgggtgaaaaaattttgaagtcaatattagcttcatcttttgcaattcttgtgtgtt

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatgg----tgtattgctcctga----------ttgattgctacattaagccat---aatagtgtctgatatccatatagtgtgcccc----actttgtcatatagtagttgttttgtt----------------------------------
  |   || || || || ||||| || |||||| | || || || ||||| |||||||| ||||||||||| |||||||||||||| || ||||||||||||         | ||||    || |          || |||||| |   |   |||    ||| | ||| | |    |  |  |   ||     | |||  |||||| | |     ||  |                                  
TTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgta---atggtgtattgctcctga--ttgattgcta--cattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt----
      || ||||| || |||||||| |||||| | || || || ||||| || ||||| || |||||||| |||||||||||||||||||| |||||||||    ||  ||  ||  ||   |  || | |  |   |   | |  |   ||  || ||| |||  |  ||  |    |  ||  ||| ||  | ||| | | |||    
TTGCCTGACGGACGAGAGGAGTCTGTTATGAAGCGGACCACTCTCGTGGCCAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatct-tgaaggattttacg-ttcatcacatt-ttgttatct-gttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctc----------ctgattgattgctacattaagccataata----------gtgtctgatat-ccatatagtgtg---------ccccactttgtcatatagtagttgttt--tgtt----
  |   ||||| |||||||||||||| |||||| | || || || ||||| ||||| || ||||||||||| |||||||||||||| || || || |||||| ||  | | ||  ||          ||   |   ||||  || || ||||   |           ||| ||| || | ||   || ||           || | |  | ||  |   | |||||  ||||    
TTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcag

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 12
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt
      |||||||| ||||||||||| |||||| | ||||| || || ||||| || || || |||||||| || || || |||||||| ||||| || |||| ||   |     | | |  | |  |||   || | |    || || || |                                               
CTCCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgta-tgtccttccaattcaggctcaacgctgattttatc---gatggtttcag-----------------------------------------------

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 11
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt
      |||||||| ||||||||||| |||||| | ||||| || || ||||| || || || |||||||| || || || |||||||| ||||| || |||| ||   |     | | |  | |  |||   || | |    || || || |                                               
CTTCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgta-tgtccttccaattcaggctcagcgctgattttatc---gatggtttcag-----------------------------------------------

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|58660984|gb|CK049664.1|CK049664
EST:     TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAG                         GAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
genomic: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
EST: gi|58653094|gb|CK041774.1|CK041774
EST:     TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAG                         GAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
genomic: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
EST: gi|58674416|gb|CK063102.1|CK063102
EST:     TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAG                         GAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
genomic: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
EST: gi|27547953|gb|CA765929.2|CA765929
EST:     AACGCATCCAACATGCCTGTCGCTGCTCGNGAAAGCTTNCATTTTT-CAG                         GNATTACGATAGCTGNGT-TTANCGGGACATGGGT
genomic: AACACATCCAACATGCCTGTCGCTGCTCGTGAA-GCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGT

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), 71 (downstream exon)
Score: 15

ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctgattgattgctacattaagccataatagtgtctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccccac