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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT

Basic information

species Oryza sativa
transcript LOC_Os02g07760.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G128114_T03 (Zea mays), 3'ss of exon 9
-----agtgagtaaggtcat---ttcactttatgtaaattatatgtttttagt--gaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
       |||  |  ||| |   || |   | ||||   | | |  ||| |||  ||| | ||| ||  |          || || |||     |  | |||||||  |||| |||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||  |||||||||||
atttttttgaacatagtcttgttttgaaggtttgtatgctctgtcatttcagtctgagaccttttaatga----------tgatgctcacaaaaaataattattttttagGTCTCTTTGGAACTTGGTGGGAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCTGTTAAAGGCAGT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 10
-agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgata-agttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
   |    ||  |  | |   |||       ||  ||| | |        |  |   | |   |    |  || |   ||     | | | | || ||  |||| || ||||| |||||||| |||||||||||||||||||| |||||||| ||||||||||||||  |||||||||||
gttttttgaacatggtcttgttttg-aaggtttgcatgctct-gtcatttcagtctgagacctagtgatgatgctcaccaaaaaaaaacaataatgttgtagGTCTCCTTGGAACTTGGTGGGAATGCACCTTGCATTGTTTTCGATGATGCGGACATTGATGTTGCTGTTAAAGGCAGT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
     ||| | | |  |   ||  ||| ||||   | ||   |   ||| | |  | |     |  ||     | |  ||||   |   | |  || ||||| ||| | || || || ||||||||||||||||| |||||||||||||| ||| | ||||||||  | ||||| | |
-----gtatgcttagat--attgttgtgaatt---tcttcaaatacaggatctatacatcttgatcttatatatatatatgccttt---tgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G17450.1 (Glycine max), 3'ss of exon 10
agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
     ||| | | |  |    | |||  ||||      ||  | |      ||  ||  |      || |   | |  ||  ||     | |  || ||||| ||| | || || |||||||||||||||||||| |||||||||||||| ||| | ||||||||  | ||||| | |
-----gtatgcttagatattgtcatg--aatttc----ttcaaatacaagattagaaggattttttttaccattatatata-tgccttttgaacttccagGTATCTCTTGAACTCGGTGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S6_180V6.1 (Physcomitrella patens), 3'ss of exon 9
agtgagtaaggtcatttcactttatgtaaattat----atgttttta-gtgaggct---tttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT-
    |  |   | | || ||| |||| |  || |     |||||||   || | ||     |   |  | || |||     ||   | | || || |        |||||||| || ||||||||||| || ||||| ||||| ||||||||||||||  |  | || |||||  ||||||| ||| 
--ctacgagatttacttaactgtatggattttttccgggtgtttttgcatgtgactgaacctgcgaccagaatattctccttgacaaagatggtatgc------gcagGTTTCCTTAGAGCTTGGTGGTAACGCACCGTGCATCGTTTTTGATGATGCTAATTTGGACGTTGCTGTTAAAGG-AGTG

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|163925517|gb|EG715386.1|EG715386
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218498176|gb|FG949780.1|FG949780
EST:     CAGCTGTTGGC-AAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218492832|gb|FG951181.1|FG951181
EST:     AGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACCTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAA
genomic: AGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATAC-TGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAA
EST: gi|88288968|gb|CI520298.1|CI520298
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218482143|gb|FG968613.1|FG968613
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218492318|gb|FG946726.1|FG946726
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|88519470|gb|CI447124.1|CI447124
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218490731|gb|FG966180.1|FG966180
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|66918914|gb|CX105762.1|CX105762
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         G-TTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTG
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTG
EST: gi|58694576|gb|CK083263.1|CK083263
EST:     AGCTGTTGGCNNNNNNNCTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: AGCTGTTGGC-AAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218491346|gb|FG955033.1|FG955033
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTGTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA

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), 67 (downstream exon)
Score: 37

GTCAGAAAGATTACATTCACAGGGTCAACAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
                                  tgctgat  putative branch site (score: 37)
                                            ttatttt  putative PPT
     ttttcaaaaaaaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgc