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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttgggctaattatgtgtttatgtatttaaaag

Basic information

species Oryza sativa
transcript LOC_Os01g40340.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttg--ggctaattatgtgtttatgtatttaaaag---
||||| |||||||||||||||||||| ||||| |||||||||||  |||| ||||||||||| |||||  ||||||||   ||||  |||  |  | ||  | | || |||||| |||  | |  |    ||||||  | ||||| |||| |||   
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaaa--tgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag

upper sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA15G13580.1 (Glycine max), 5'ss of exon 18
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatctta----aaacatactttggtatctttggtttttttgtccttgggctaat-tatgtgtttatgtatttaaaag------------------------------------------------------
||||||||||||||||||||||| ||||| || || ||||||||  ||||  |||||||||| || ||  ||||| | |||  | |      | ||||| |  ||   |||   |  |||||  |||  ||    |   || |     || |||| |                                                      
GATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAGgtaaatggtgtgcctctgttgatcatacatgtgtcaatttt-ctactttgtatttgaactgtcatgcctggtgtctcatgtaaaggtctttattccaattctttcaatgtataccttagattttgctttgacacatgcag

upper sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 18
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatt--------tgtgatcttaaaacatactttggtatctttggttt---ttttgtccttgggctaattatgtgtttatgtatttaaaag----------------------
|||||||| |||||||||||||| ||||| ||||| ||||| ||  |||| || |||||||| |||||  ||||||         |||  | |      | |  ||  |  | ||| ||    |  | | |||| |||   | || ||   |  | |||  |                       
GATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAGgtaatcggttcaactgttttttcctggtagaaattaat-ccgttgattcgcatcatatgcttgagcttgatgtg-gtcccttaacttacgaaatataacatggtgtcgttgcag

upper sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 5'ss of exon 18
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctt---tggtttttttgtccttgggctaattatgtgtttatgtatttaaaag----------------
|||||||| |||||||||||||| || || || || |||||||| |||||| ||||||||||||||||  ||||  | |    | | |     || ||    |  |   || |   | | |     |   ||  |       | | | |   |||                
GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAGgtaggtggaagcccttattttgaccttctccttctatatgatacctatttaaaatgaaaaaaaaaaaaaaaaagcaatctgaaggtcttctccattgtcc

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|38473714|gb|CF957846.1|CF957846
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGAT-G                         --GTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
EST: gi|58691100|gb|CK079787.1|CK079787
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         ---TTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
EST: gi|8956745|gb|BE230548.1|BE230548
EST:     GTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         CAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
genomic: GTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
EST: gi|29680806|gb|CB677081.1|CB677081
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         ---TTCCCTCTTTAC
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTAC
EST: gi|88694640|gb|CI738678.1|CI738678
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         CAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         CAGTTCCCTCTTTACAAATTCG
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCG
EST: gi|29680847|gb|CB677122.1|CB677122
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         ---TTCCCTCTTTACAAATTCGAATTGGTTTACATTTGAT
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGAT
EST: gi|88327344|gb|CI645125.1|CI645125
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         CAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGG

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: 50 (upstream exon), 73 (downstream exon)
Score: 5

GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... tatttaaaagCAGTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTATTACTGACCGTTTGGCTGCGGTTCCTTCGTCTTCACCTAATTCAGAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttgggctaattatgtgtttatgtatttaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG