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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaaccgccttatttctctgttacatatgcttcttgttttatttaaaagaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacag

Basic information

species Oryza sativa
transcript LOC_Os08g23810.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G125052_T01 (Zea mays), 5'ss of exon 10
GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaaccgc---cttatttctctgttacata-tgcttcttgttt-tatttaaaagaacaa--cttttcatccagata-------tactctaacgaaagcattttgtatgtcgaacag
| ||| | || ||||||||||| |||||||||||||| || |||||||||||| | ||||| |||||||||||||| |||||||| ||||||||||| |||| | |   ||   |||  ||   ||| || |  || ||| |     ||||| ||||  | |  |||||  | || |         |  | |||| || | | | |   ||| | ||||
GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATCGAGAAGATGATATAGTACTCATATGTTAATGCACCATTGCAGAAGGAACTGTTGGCTGgtc-agagttgcatactttgttacttgtcacttgctgtttcctccccgtatttgaaaggtccaacctttttcttcaaacgctgtcttttttttaacaaatgtactct---tgttggacag

upper sequence: LOC_Os08g23810.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G070422_T03 (Zea mays), 5'ss of exon 11
GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc-gccttatttctctgttacatatg-cttcttgttt--------tatttaaaaga--acaac--ttttcatccagatatactctaac------gaaagcattttgtatgtcgaacag
| ||| | || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||||||||||||| |||||||| || |||||||| ||||  |     | ||  |  || |||||| | || |||  |||||        ||||| ||||    ||||  ||||| ||    |   ||||           ||| ||  | | ||| ||||||
GCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTGgtcagagttttgactcctccctttgttacttgtgacttgctgtttcatccccctatttgaaaggtggcaacctttttcttcacagtgctctcttttttcttaacaagtatgctct-tgttgaacag

upper sequence: LOC_Os08g23810.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ10940 (Selaginella moellendorffii), 5'ss of exon 10
GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaaccgccttatttctctgttacatatgcttcttgttttatttaaaagaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacag
|||| |||  |||| |||||||||||||||| |||||||||||||||||||| || |||||  | |  ||  | ||  |||| | ||| ||    || ||| |   |    |||     |   || | |    | |||  ||   |  | |      ||||||   |||                                    
GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTGgtgcgttaaaaactttggcttggcttgcttggtttgcttacttcgctatatact----cttttcgcacag------------------------------------

upper sequence: LOC_Os08g23810.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ25882 (Selaginella moellendorffii), 5'ss of exon 10
GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACT----GTTGGCAGgtccaaaaccgccttatttctctgttacatatgcttcttgttttatttaaaagaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacag
|||| |||  |||| |||||||||||||||| |||||||||||||||||||| || |||||  | |  ||| | ||  |||| | ||| ||    | ||| | || ||||||       |  || || |   | |||||  |    ||| ||         ||||||   |||                                    
GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAATTCTCCCCTGCAAAGAGATCTCGAAGCTGgtacgttcaaaactttggcttggct-tgcttggtttgcttacttcgctatatact-------cttttcgcacag------------------------------------

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|88487859|gb|CI425130.1|CI425130
EST:     GAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|88672973|gb|CI727088.1|CI727088
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|29613729|gb|CB618742.1|CB618742
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|3767353|gb|AU031463.1|AU031463
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAA-TGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|33691059|gb|CF319298.1|CF319298
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|88262025|gb|CI365601.1|CI365601
EST:     GATAGAATACTCTTATGTTAATCCACCGTTCCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA

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: 68 (upstream exon), 75 (downstream exon)
Score: 17

GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTATCACTGGCTCGACTGTTTACGTTGACAATGGACTCAATACAATGGGGCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaaccgccttatttctctgttacatatgcttcttgttttatttaaaagaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC