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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttatgtactggtgtatattgttatctttgtattgaaaattgtgaacttcttagtttattgcctaggaaaagtaatagttatctttcttaatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 10
--tgttatgtactggtgtatattgt----tatctttgtattgaaaatt---gtgaacttcttagtttattgcctaggaaaagtaatagttatctttcttaatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG
   ||| | |    || || || ||    ||    | |||  | | ||   ||| || ||||   |  || |  ||||||  ||||  ||  | |||       | ||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||||||| |||
gaagttctttgtgtgtatacatagtgaagtaatactatatatatagttttagtgcacatcttgcctctttccacaggaaac-taat--ttgacattca------attagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 10
tgttatgtactggtgtatattgttatctttgtattgaaaattgtgaacttcttagtttattgcctaggaaaagtaatagttatctttcttaatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG
   | |||| |  |   |||| | |       | |       |||   | |||     | | |  |  | || |  |   | ||||||||    || ||||||||||| ||  |  | ||  ||||   |||||| |||||||| || || || |||||||| ||||||||||||||| | |||
aactttgtaatcattattattatgaatagatcactctgctgagtggtatacttgagcaaattcagaaaataaattctttgtttctttcttctcacattagGTACATCGCGTGCTTGTGGATCTTGTTTCTGCTTCTGCAAATGCAACGCCTGGTCTTGGAAGGTATCCTCCATTCAAGAGAGAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 10
tgttatgtactggtgtatattgttatctttgtattgaaaattgtgaact----tcttagtttattgcctaggaaaagtaatagttatctttcttaatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG
     |  |      ||| || |  |   |   || ||| |  || |      |  |   |||||  |  |   |  ||| | |  ||||   |  || | ||||| || || ||  |  | ||||| ||    ||||| |||||||| ||||| |||||||| ||||||||||| |||||||| |||
--ccgtagatgtagctattttttggttcctactttaaaactcatgcatccagcttctgtcttatttacgtgttgagctaaca-tggtcttaacttttg-attagGTTCACCGAGTTCTTGTTGACATAGTTTCAGCTTCTGCAAATGCTACACCTGGACTTGGGAGATATCCTCCTTTCAAGCGAGAG

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|88334745|gb|CI676538.1|CI676538
EST:     GATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAG                         GTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
genomic: GATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAGgtatgttcta ... aatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
EST: gi|88405106|gb|CI685555.1|CI685555
EST:     GATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAG                         GTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
genomic: GATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAGgtatgttcta ... aatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
EST: gi|88585403|gb|CI703033.1|CI703033
EST:     GATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAG                         GTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
genomic: GATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAGgtatgttcta ... aatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
EST: gi|29622847|gb|CB627858.1|CB627858
EST:     AGATAGTATTGGATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAG                         GTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
genomic: AGATAGTATTGGATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAGgtatgttcta ... aatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
EST: gi|58668422|gb|CK057108.1|CK057108
EST:     AGATAGTATTGGATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAG                         GTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA
genomic: AGATAGTATTGGATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAGgtatgttcta ... aatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttcttagtttattgcctaggaaaagtaatagttatctttcttaatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG
                                         tcttaat  putative branch site (score: 3)
                                     tctttctta  CT-rich tract
                       aaaagtaatagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttatgtactggtgtatattgttatctttgtattgaaaattgtgaacttcttagtttattgcctaggaaaagtaatagttatctttcttaatgcactagGTACATCGTGTATTGTTAGACATTGTCAATGCTTCAGCAAATGCCACACCAGGACTTGGAAGATATCCTCCATTCAAGCGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA