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

TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttgtggtgttttgaacattttgc...

Basic information

species Oryza sativa
transcript LOC_Os08g42410.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G043198_T03 (Zea mays), 5'ss of exon 7
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataacca----atatt-tgtggtgttttgaacattttgc
||||||||||||||||||||| ||||| ||||||   ||||||||||| ||||| || ||||| |||||||||||||| |||||||| || ||||| ||||||| || || ||| ||     | | |   || | |  |   ||  | ||||| ||| || | |||||    |    | ||  | |  | || ||||  | ||  
TGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTGCTGGAGTTGGTGCCCAACACTCACAGgtttttg-cacaaagtttcctctacatgggtgctctgttg--ctgctgttattctttagaggacaaattgttatgccacatgatttaattttctgaaagtctt--

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttg----tggtgttttgaaca-ttttgc----------
 || || || ||||||||||| ||||| || |||   || |||||||| |||||||| || || ||||| |||||||| |||||||||||||| ||||| || ||   |    |  || |      ||      |   |  | ||  | ||||        |  ||||||   |  |||     | || |    ||||  |||||          
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttattta--actatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 7
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttgga---cggcaaataaccaatatttg----tggtgttttgaaca-ttttgc----------
 || || || ||||||||||| ||||| || |||   || |||||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| ||  |   |     |||| |  |  || | |        | | |||| | | | ||||      |  ||||||   |  |||     | || |    ||||  |||||          
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGGGTTGGTGCTCAGCATTCTCAAgtacggttc---tccttgctgctttctttttaaagacaaactttatt-taactatttgagaactgataaataattcaggttttgtctttgtatgcccaacaactttgcctttatgcag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 7
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttg----tggtgttttgaacattttgc-----------
 || || || ||||||||||| ||||| || |||   || |||||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| ||  |   |    |  || |      ||      |   |  | ||  |  |||        |  ||||||   |  |||     | || |    ||||  ||             
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGGGTTGGTGCTCAGCATTCTCAAgtacggttctcctagctgctttcttttaaagacaaactttattta--accatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaacttttcctttatgcag

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttgtggtgttttgaacattttgc--
||| ||||| || |||||||| ||||| |||||||| || || || || |||||||| || || |||||||||||||||||||| ||||| || ||||||||    | |  |  |     ||     ||   || ||   ||  ||| ||        |||    |   || || | |  |   | | |  | ||       
TGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGTGTTGGAGCTCAACATTCTCAGgtaaacg-ctcacccaaaaaaaattgaataatttgttactttgcattctttcaaaagagaccttcagctactaa-actgataaagatattcatataggatga

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 7
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttgtggtgttttgaacattttgc-
||| ||||| ||||| ||||| ||||||||||||   || || |||||||| ||||||||||| || |||||||| || |||||||| ||||| |||||||| |    || |  ||   | || | |||   |||| | ||| |   || ||  | |||   |       | ||  ||   | || | ||   ||||| | 
TGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTGCAGGAGTTGGTGCCCAGCATTCTCAGgtgtagtccaaattctgtctgatacttattgtttatgcgattttgccatcat-atatggttagtctccttctaaccttctagatgctctgcttattttccc

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 8
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttg-tgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataacca--atatttgtggtgttttgaacattttgc
||| || || ||||||||||| ||||||||||||  ||| ||||||||||||||||| ||||| |||||||| ||||| |||||||| |||||||| |||||    |  | ||   ||  |  |||  | ||| |    | || | | |  |   |||         ||  ||    |  |  |   | |   |||||  || 
TGCAAAATCAAACTACATGTCCGCTGGTCAGATATCCGTACCTATTGTTTTTAGAGGACCAAATGGTGCTGCCGCTGGAGTTGGTGCCCAGCACTCCCAGgtacactccctgaggttttctcttgc--acctggtgacttgtt-tgtcaccagcttttctctatatgatgcccgtggtgctgatctggatcataacataatga

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|33824375|gb|CF338004.1|CF338004
EST:     TTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAG                         TGTTATGCGGCTTGGTATGCGCATGTACCAGGATTGAAGGTCCTAACTCCT
genomic: TTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgaca ... tggtatgcagTGTTATGCGGCTTGGTATGCGCATGTACCAGGATTGAAGGTCCTAACTCCT
EST: gi|38472326|gb|CF956457.1|CF956457
EST:     TTAGAGGACCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAG                         TGTTATGCAGCTTGGTATGCGCATGTACCAGGATTGAAGGTCCTAACTCCT
genomic: TTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgaca ... tggtatgcagTGTTATGCGGCTTGGTATGCGCATGTACCAGGATTGAAGGTCCTAACTCCT
EST: gi|218484233|gb|FG953202.1|FG953202
EST:     TTAGAGGACCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAG                         TGTTATGCAGCTTGGTATGCGCATGTACCAGGATTGAAGGTCCTAACTCCT
genomic: TTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgaca ... tggtatgcagTGTTATGCGGCTTGGTATGCGCATGTACCAGGATTGAAGGTCCTAACTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTGCTGGTGTTGGTGCTCAGCACTCTCAGgtttgtgacagaaacttgttaatgcctatctgttattctattctattattattgtttggacggcaaataaccaatatttgtggtgttttgaacattttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT