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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt...

Basic information

species Oryza sativa
transcript LOC_Os08g41460.6
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 2
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtgg------tataaaata--ttccttttcttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt
   ||||| || |||||    |||||  | |||||||| ||||||||||| ||||||||||||||||| ||||||||||| |||||||| |||||||||||| ||||        |  || ||    ||  | || | |  || ||  |   |   | |  |   ||| |||| ||  ||   | ||   ||  |  | ||       
---GCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAAgtgagtgcgtttttcactaattaagcccccctcctgcgactttttattattactgtgtcgatgacgtatactagaaacgtat-ttccttagacgacgacaa-------

upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G14240.1 (Glycine max), 5'ss of exon 3
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt
   || || ||||| ||    |||||  | ||||| ||||| || || ||||| |||||||| || || ||||||||||||||||||||||| ||||||||||  |||   ||  |    || |  ||  ||||  |   | | |     | ||  |  |  || ||   ||  ||    | |                 
---GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgta--tggggcaacttcgctctatagttgcagctgttgtcataacttcatcttt-ttaaagtctttattggttgattgtacag-----------------

upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G42360.2 (Glycine max), 5'ss of exon 3
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgta-agtggtataaaatat-------------tccttttcttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt-----------
   || || ||||| ||   ||||||  | ||||| |||||||| || ||||| || ||||| || || ||||||||||| |||| ||||||||||||||||| | |  ||| | ||||             || ||  ||   || |  ||  |          | | ||  ||  | ||| |     |     |  |   |  |  |||  |           
---GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAATCTTAAGGAAGAACTCATGTGGGAAGGGAGCACCGTTGTGATGCTAAgtatattattattatatatgtggctagcaatttcattcactgacagttgctagcatgcatgaattcctgcta-actttgtaaattgattttatttttgagtcattataattggttcgctgtgtag

upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatcccggcccttactgtacacta---taagtgtgcatgccgctgaaaagaaaaagattatt----------
   || || ||||| ||    |||||  | ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||||| | || |      | | |  |     ||||| | |   | |   | |  | | | |    ||      ||||   |  |  |   |||     | |  ||          
---GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca------acttcactctcagtagct-gcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag

upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatccc-ggcccttactgtacactataagtgtgcatgc-cgctgaaaagaaaaagattatt
    | |||||||||||    || ||  | ||||| ||||| ||||| |||||||| || || ||| | ||||||||||||||||| ||||| |||||||||||     |   |  |||  |  | || |   |  | |     ||  ||  |||  |      | ||| | |   |      || |               
---TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag--------------

upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 5'ss of exon 3
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta--taaaatattccttttcttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt
    | || ||||| ||    || ||  | ||||| ||||| ||||| |||||||| || || ||| | ||||||||||||||||| |||||||||||||||||     |  ||    | |   |||| | |   ||||    | |      | ||  || | | |   |       |   | | | | |||| | |     
---TCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAAgtaatcatcaactatgggactaaatttcatttc-tttgttttggttt-----ctttggtgcaaagtcctaaatcttttattggtaatatgaaacacag----

upper sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattcctttt----cttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt
    | |||||||| ||    |||||  | ||||| |||||||| || || ||||||||||| || || ||||||||||||||||||||||| ||||||||||  |  | || | |||     |       | ||   | ||  || |       |||  |  |      || |||  |    ||| |   | ||   |     
---TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatt-tagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag----

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|29625905|gb|CB630916.1|CB630916
EST:     AAGGAAGCAGCGTTGTGATGNTAA                         GCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: AAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
EST: gi|58595312|gb|CF993620.1|CF993620
EST:     TAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA                         GCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: TAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
EST: gi|29684942|gb|CB681217.1|CB681217
EST:     TGTGGGAAGGAAGCAGCGTTGTGATGCTAA                         GCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: TGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
EST: gi|38474705|gb|CF958838.1|CF958838
EST:     TAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA                         GCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: TAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
EST: gi|29683115|gb|CB679390.1|CB679390
EST:     GCGTTGTGATGCTCT                         TCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: GCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
EST: gi|29663222|gb|CB659497.1|CB659497
EST:     TGTGGGAAGGAAGCAGCGTTGTGATGCTAA                         GCCTTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: TGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
EST: gi|163920678|gb|EG710011.1|EG710011
EST:     TAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA                         GCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA
genomic: TAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCA

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: 75 (upstream exon), 73 (downstream exon)
Score: 71

TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggta ... ttttcgtcagGCCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCAACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA