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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgctgcaactgatataattttgttactag

Basic information

species Oryza sativa
transcript LOC_Os06g49140.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G083745_T03 (Zea mays), 5'ss of exon 5
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgt---acttttctcatatggatttggcttgct-gtattttctcccatggtttgtcttgctgcaactgatataattttgttactag
 |||||||| || || || ||||| |||||||| ||||| || |||||||| ||||||||||| || || |||||||| |||||||| |||||||| |||||   ||     | | |    | | ||||  | ||  || |  |  |    || ||      ||||  |||   |||  |   ||
TCTTCCTCTCATCGTCGCAATTGACTTGCAACCGATGGCCCCAATAGAAGGTGTTATACAAGTGCAGGGCGACATCACCAATGCTCGGACAGCAGACGTGgtgagacagaagtaaaagacgtgtagcttttttgttgttgccgcagttagctggctgtgactaactagtatggatttcctgtcag

upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G07970.2 (Glycine max), 5'ss of exon 6
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttctcata--tggatttggcttgct---gtattttctcccatggtt--tgtcttgctgcaactg-atataattttgttactag-----------
 |||||||||||||| || ||||||||||||||||||||||| || ||||| || || || || || || || || ||||| ||||| ||||| |||||||||  |    || |  |   ||  | ||  |   | ||| | |    |||    ||| |||    | ||| || |  |  |   | |||           
TCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAACGCTCGGACAGCTGAAGTGgtatatacagcagaattaccttcagttttttcatggattattttatttggaagatgtgttgagtaagctgcatgtcttggtagaaatagaaaatacatct

upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G31350.1 (Glycine max), 5'ss of exon 1
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgct--gcaactgatataattttgttactag--------------------
 |||||||||||||| || ||||||||||||||||||||||| || ||||| || || || || || || || || ||||||||||| ||||| |||||||||  | |   |||| |  |    || |  || ||| | | || | || | ||  |  | || ||   | |    | | |  |                    
TCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACAGCTGAAGTGgtatatattatatatagcat--aattaccttagttttttc-atagattattttatttggaaaatgtgttgaacaagctgcatgtctaggtagaaatagaaaat

upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G31380.1 (Glycine max), 5'ss of exon 6
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttctcatatggatttggcttgct-gtattttctcccatggtttgtcttgctgca---actgatataattttgttactag---------------
 |||||||||||||| || ||||||||||||||||||||||| || ||||| || || || || || || || || ||||||||||| ||||| |||||||||  | |   |||| |  |   |    | || |||||    ||  |||   |||    |     |||   |  |   |  ||||               
TCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACAGCTGAAGTGgtatatattatatatagcataatcaccttagttttttcatagattattttatttggaagatgtgttgaacaagctgcatgtctaggtagaaatagaaaat

upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G01230.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgta-----------cttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgctgcaactgatataattttgttactag----------------------------
 ||||||||||| || ||||| |||||||| || |||||||| || ||||| || || || |||||||||||||| ||||||||||| || || |||||||||           ||  | ||  ||  ||||  ||   | | |||  |||  |  ||  |  |||| ||| |  | |  || | |   | |                            
TCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctct--ttaattatgcttcaagtt-tgtgtttgtttccatggcttaccttttccggtgttttttttcaag

upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 5'ss of exon 5
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgt------acttttctcatatggatttggcttgctgtattttctcccatggtttg----tcttgctgcaactgatataa--ttttgttactag-------
 |||||||||||||| || ||||||||||| || |||||||| || ||||| || || ||||| || || || || || |||||||| ||||| ||| ||||      | || || |     |   | | |  |  |  ||| |   |  || |     | |   ||   ||  | |||  || ||| |||         
TCTTCCTCTTATTGTGGCGATTGATTTGCAGCCCATGGCTCCAATTGAAGGGGTGATTCAAGTCCAGGGTGATATAACAAATGCTCGTACAGCTGAACTGgttagtcaatttctccccccaagtcattgttatccattatttgtttgacagtgtaaagatataaatggcgcttctttaaaattatgtaactgatttaata

upper sequence: LOC_Os06g49140.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ07303 (Selaginella moellendorffii), 5'ss of exon 5
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgctgcaactgatataattt-tgttactag
 |  ||||||||||| || ||||||||||| |||||||| || || || || ||  | ||| ||||||| |||||||||| ||| ||||| || ||  ||||       |  || | || |    |  | | |  | |   | | | | | || ||     ||   |  ||| |  |  |||
TCGACCTCTTATTGTGGCTATTGATTTGCAGCCAATGGCCCCTATTGATGGTGTCGTTCAAATTCAAGGAGACATCACTAGTGCACGAACTGCCGAGTTGgt-------tggta-gaatctcaagtattatgtaatgtttgaagctctttttttctttttttgtggttttttgtcctcgtag

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|218502657|gb|FG948620.1|FG948620
EST:     CAAGTTCAAGGGGAC-TCACTAATGCTCGAACAGCAGAAGTG                         GTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGT
genomic: CAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttct ... ttgttactagGTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGT
EST: gi|66924739|gb|CX111587.1|CX111587
EST:     GCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTG                         GTTATTAGGCATTTTGATGGAT
genomic: GCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttct ... ttgttactagGTTATTAGGCATTTTGATGGAT
EST: gi|27547118|gb|CA765118.2|CA765118
EST:     CATCACTAATGCTCGAACAGCAGAAGTG                         GTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGT
genomic: CATCACTAATGCTCGAACAGCAGAAGTGgtacttttct ... ttgttactagGTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGT
EST: gi|27920673|gb|CB096481.1|CB096481
EST:     CAAGGGGACATCACTAATGCTCGAACAGCAGAAGTG                         GTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGT
genomic: CAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttct ... ttgttactagGTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGT

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), 61 (downstream exon)
Score: 10

CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttct ... ttgttactagGTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGTGCTCCTGATG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACAGCAGAAGTGgtacttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgctgcaactgatataattttgttactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT