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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgagtgaaacaacatctgccagttatgtaatgcatgtcactatcacaagccttcaatatgtaggaactaatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC

Basic information

species Oryza sativa
transcript LOC_Os06g48650.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 6
-------aatgagtgaaacaacatctgccagttatgtaatgcatgtcactatcacaagccttcaatatgtaggaac-taatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC
       ||  |     |        |  |  |   |  |  |      | |   |||| | |||| ||| ||||  ||||||||| ||| | ||       ||||||||||| ||||||||||||||||||||||||||||||||||| || |||||||| ||||| ||||| |||||||| ||||||||||||||||| |||||||
catgtagaacaaacatgaagttgaacgt-aacttcattttctactaagttttttaaagcatccaatttgtgggaatataatgcatgaatgtctat-------ttgcagGCTGTTCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGGCCCAATAGCCCACCAACAGCTACACGGACTACTTTTTTGAATCCTTTTGACGCTGCAC

upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G099452_T01 (Zea mays), 3'ss of exon 6
--aatgagtgaaacaacatctgccagtt--atgtaa-tgcatgtc---actatcacaagccttcaatatgtaggaac-taatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC
  ||  |||| ||||| |  ||  ||||  |||||| | ||| |      | |   |||| | |||| ||| ||||  |||| |||||||| | ||       ||||||||||| ||||||||||||||||||||||||||||||||||| || |||||||| ||||| |||||  ||||||| ||||||||||||||||| |||||||
ctaaacagtggaacaa-acatga-agttgaatgtaacttcattttctagtttttttaagcatccaatgtgtgggaatataatccatggatgcctat-------ttgcagGCTGTTCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGACCCAATAGCCCACCAACAGCTACAAGGACTACTTTTTTGAATCCTTTTGACGCTGCAC

upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 5
aatgagtgaaacaacatctgccagttatgtaat---gcatgtcactat-cacaagccttcaatatgtaggaactaatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC
    |||  ||||  | |   |||||||  | |     || |  |||      ||  ||  || |  ||   |   |  ||   |   | |    |     ||||||||||| ||||| || || || |||| |||||| ||||| |||||||| || ||| |    ||    ||||||||||||||||||||||||||| |||
--ctagttcaacataaacaatcagttatacagtcttatatttttctaagtgttagtattttatctcaagatgcc--ttaattatttatatttgaaaacgaacagGCTGTGCATGATGGGGTGGATATACTCAGCCTTTCAGTTGGACCAAATAGTCCTCCATCAAACACCAAAACTACATTTTTGAATCCTTTTGATGCTACAC

upper sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 6
---aatgagtgaaacaa-catctgccagttatgtaatgcatgtcactatcacaagccttcaatatgtaggaactaatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC
         ||||  || |||||     ||| || ||   |||     |        ||   | | |      | ||  || || | |  ||| |  |   |||||||| || |||||||| ||||||||||| || ||||| || |||||||| || ||| |  | ||   ||| || ||||| || ||||||||||||||||
ttttgcccatgaattaagcatcttt---ttaggtgatatctgttggggtattctttgttttttgttttttcgtttattaattgaagact-tcttctgtgaacagGCTGTTCATGATGGTGTGGACATTCTCAATCTCTCTGTGGGGCCAAATAGTCCTCCAGCAACCACCAAGACCACGTTTTTAAACCCTTTTGATGCTGCAC

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|88720601|gb|CI743900.1|CI743900
EST:     ACAGGCTTTTTGGTGGTTATGTATCTGATGTTGTTGCAGCCATTGATCAG                         GCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC
genomic: ACAGGCTTTTTGGTGGTTATGTATCTGATGTTGTTGCAGCCATTGATCAGgtataacata ... cattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC
EST: gi|163922990|gb|EG712763.1|EG712763
EST:     ACAGGCTTTTTGGTGGTTATGTATCTGATGTTGTTGCACCCATTGATCAG                         GCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC
genomic: ACAGGCTTTTTGGTGGTTATGTATCTGATGTTGTTGCAGCCATTGATCAGgtataacata ... cattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC
EST: gi|58681743|gb|CK070430.1|CK070430
EST:     ACAGGCTTTTTGGTGGTTATGTATCTGATGTTGTTGCAGCCATTGATCAG                         GCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC
genomic: ACAGGCTTTTTGGTGGTTATGTATCTGATGTTGTTGCAGCCATTGATCAGgtataacata ... cattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC
EST: gi|58684518|gb|CK073205.1|CK073205
EST:     ATCTGATGTTGTTGCAGCCATTGATCAG                         GCTGTGCAGGATGGTGTTGACATTCTCAAGCTTTCTGTTGGCCCAAATAGC
genomic: ATCTGATGTTGTTGCAGCCATTGATCAGgtataacata ... cattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaagccttcaatatgtaggaactaatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC
                     aactaat  putative branch site (score: 2)
        ttcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgagtgaaacaacatctgccagttatgtaatgcatgtcactatcacaagccttcaatatgtaggaactaatgcatggatggcaatctgcattttgcagGCTGTGCAGGATGGTGTTGACATTCTCAACCTTTCTGTTGGCCCAAATAGCCCGCCAACTGCTACGCGGACTACATTTTTGAATCCTTTTGATGCTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC