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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttactaatgttgatcttaaatatttgtaatgtctacttgtactgcaagtgtcttattttaacagatgagaatggagtctatggtgatatactatt...

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 2
GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttactaatgttgatc-ttaaatatttg-----taatgtctacttgtactgcaagtgtcttattttaacagatgagaatggagtctatggtgatatactatt
||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| ||| |||||||||| || ||||||||||||||||||||||| ||||| ||  ||  |   ||  |   | | ||      ||| |  | | || ||| |  | |   | || |  ||  | | |   || ||    | | |       
GATGATGGGTCACCTGTGTCAATTTTTTCTCTGTCAGGGAGCAACCCTCAGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaacaacttcagtcactgggtttctgattaccaatattcaatagtgctgtaccttttagacttgaggagcagtgtacaaagccttctttcagaa------

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 2
GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttactaatgttgatc-ttaaatatttgtaatgtctacttgtactgcaagtgtcttattttaacagatgagaatggagtctatggtgatatactatt--
|||||||||||||| |||||||| |||||||||||||||||||| ||||||||||| ||| ||||||||||||| || |||||||||||||||||||||||||| ||  ||  |   || ||   | ||| || |  | |  |  | |     |||    |||  ||   |||| | | ||||| |||||  | | | |   
GATGATGGGTCGCCTGTGTCAATTTTTTCTCTGTCAGGGAGCAACCCTCAGGACAGACACATGGTTGCTGGTCGCAACGGTGTTAAGAGATTACGAACAgtaagctaacaacttcagtcattgggtttttttattaccgatattcaatagtgatgtaccttttagact--tgagga-gcagtctttggtggcaaaatgtcaa

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 5'ss of exon 2
GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttactaatgttgatc---ttaaatatttgtaatgtctacttgtactgcaagtgtcttattttaacagatgagaatggagtctatggtgatatactatt
||||||||||| |||||||| || |||||||| ||||| || ||| |||||||  | || || | |||||| || |||||||| ||| |  | || |||||||| ||| |||| | ||    ||   ||| |   ||    |   ||  |     | |   |||||  |   |    ||  | |||||||   | || |   
GATGATGGGTCTCCCGTGTCTATATTTTCTCTTTCAGGAAGTAATGCTCAGGATGGACATTTAGCTGCTGGCCGTAATGGTGTCAAGCGTCTTCGCACAgtaagctaccaatgattattactttggctatattagatacaaatgagtttttttcctttgcaattttgcct--ttgtgatatattctatggatttttaattc-

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|88731434|gb|CI755047.1|CI755047
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAG
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAG
EST: gi|117245083|gb|CT843332.1|CT843332
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88407897|gb|CI588926.1|CI588926
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACA
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACA
EST: gi|58695768|gb|CK084455.1|CK084455
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|58695973|gb|CK084660.1|CK084660
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|25804372|gb|CA760333.1|CA760333
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|58690937|gb|CK079624.1|CK079624
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|29636110|gb|CB641119.1|CB641119
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88427152|gb|CI586700.1|CI586700
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAACAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|29622867|gb|CB627878.1|CB627878
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|58658376|gb|CK047056.1|CK047056
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88364351|gb|CI612300.1|CI612300
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATC
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATC
EST: gi|58665117|gb|CK053803.1|CK053803
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88401421|gb|CI585977.1|CI585977
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAACAGATTACGAACA                         GTGCGTCATCCAAACATTTTATC-TTTCTTCACAGTACTGAAGCA
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCA
EST: gi|88415228|gb|CI584051.1|CI584051
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88391809|gb|CI603328.1|CI603328
EST:     AGGACAGGAACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTT
EST: gi|29676650|gb|CB672925.1|CB672925
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88391301|gb|CI595555.1|CI595555
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAG
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAG
EST: gi|88364900|gb|CI614518.1|CI614518
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAATAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
EST: gi|88410217|gb|CI575815.1|CI575815
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACA
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACA
EST: gi|29623070|gb|CB628081.1|CB628081
EST:     AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA                         GTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT
genomic: AGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTT

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: 59 (upstream exon), 69 (downstream exon)
Score: 34

GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttact ... cttattgcagGTGCGTCATCCAAACATTTTATCCTTTCTTCACAGTACTGAAGCAGAAGTTCCTGATGGACCTGCCATGAAGCATACAATTTATATTGTAACAGAGCCTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttactaatgttgatcttaaatatttgtaatgtctacttgtactgcaagtgtcttattttaacagatgagaatggagtctatggtgatatactatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA