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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacag

Basic information

species Oryza sativa
transcript LOC_Os04g58880.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G046590_T01 (Zea mays), 5'ss of exon 5
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaag-gatttttctctt--------atctactgt-atggtgcaacatgcctctggtgacacct---tttgctttaaacag
|||||| ||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||  ||||  |||           ||| |||| |||||  | |||  |||||||||||  |   | ||||| | ||||
CTTGGGCGTTGAAAAACTTAGCAAAGATGAAGTGCAGAAAATGCCGTGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCATTTCATGCGAATTGCTgtaagtaatttccctccctccctcaggtcttctgttatggtatagcattgctctggtgacatttgcctctgcttgagacag

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G17500.1 (Glycine max), 5'ss of exon 2
-CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttt-------tctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacag
 |||||  ||||||||||| ||||||||||| || || ||  | | ||||||  |||||||  | ||||| || || |||||||| |||||||| |||||||||||     |       |   | |  || | |||  |   |  | | | |    |  |  ||    || |||||
GCTTGGA-GTTGAAAAACTAAGCAAAGATGATGTTCAAAAGCTACAATGGGAGGTTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATTGCTgtaagaccactgtcaaatttgttcacatattttatctttatattttcatttaaatatgcaattgtacttgaacag

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G05040.1 (Glycine max), 5'ss of exon 5
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctcttatctactgtatggtgcaacatgcctctggtgacacctttt--gctttaaacag----
 || ||||| || |  ||||| |||||||| || || ||||||| ||||||  |||||||| | || || || ||||||||||| | |||| ||||||||||||| ||   | |   ||  | | |   |||    ||   |       || ||||    ||||| |       
ATTAGGTGTGGAGAGGCTGAGTAAAGATGATGTTCAAAAAATGCAATGGGAGGTTTTGGAGGCAAAGATTGGAAATTGGATTCATTACATGAGAATTGCTgtaag-atgaatataaaattcatttttatgtgtcctattttttccaatgcatctttctaactttacatgagtag

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 5
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttt-------tctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacag
  | |||||||| ||||| ||||||||||| || || ||  | | ||||||  |||||||  | ||||| || || |||||||| |||||||| |||||||||||     |       |   |||  || | | |  |      | | | |    |  |  ||    || |||||
GCTTGGTGTTGAGAAACTCAGCAAAGATGATGTTCAAAAGCTACAATGGGAGGTTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATTGCTgtaagaccactgtcgaatttgtttacatattttttattttttttttcatgtaaatatgctattgtacttgaacag

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacag------------
 ||||| ||||||||||| |||||||| || || ||||  ||||  |||||| |||||||| | ||||| || |||||||| || |||||||| ||||||||||| | | |  |      |         |  ||||||  | || |  ||| |||  ||  | | |             
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgt-tttgtt--cacttttaactcaagatattttgttcaacag

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 5
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctcttatctactgtat----ggtgca--------acatgcctctggtgacaccttttgctttaaacag------------------
 |||||||| ||||| || ||||||||||| || ||||| |||| ||||||  |||||||| |||| || |||||||||||||| |||||||| ||||||||||| || | | ||  || | | | |     |||| |         ||||| | |    | | ||  |  |  ||                      
ATTGGGTGTGGAAAAGCTTAGCAAAGATGATGTTCAGAAGATGCAATGGGAGGTTTTGGAGGCTAAGATTGGGAATTGGATTCATTTCATGCGGATTGCTgtaagaatatatgtcaaatttgcgggaatttaggtgtattaaatttgcatgcatttatgtatatctgctcttccaattctgttattttacataaacag

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g02340.t01 (Vitis vinifera), 5'ss of exon 5
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctc-------------ttatctac-tgtatg-gtgca-acatgcctctggtgacaccttttgctttaaacag------------------------
 || ||||| |||||||| |  |||||||| || ||||| ||||  |||||| |||||||| |||| || || ||||||||||| |||||||| |||||||||||| |||                  |||| |   ||| || |||      ||  | ||   ||   ||||   |||| |                          
ATTAGGTGTGGAAAAACTTACTAAAGATGATGTCCAGAAGATGCAGTGGGAAGTTTTGGAGGCTAAGATTGGAAATTGGATTCATTTCATGCGGATTGCTgtaagggtttactaggaactggataggattatttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtacgtattttctcttaatccagccatttcatcatgcttgtaacag

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|29669620|gb|CB665895.1|CB665895
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|29630823|gb|CB635832.1|CB635832
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|86821957|gb|CI309340.1|CI309340
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGTTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|58663378|gb|CK052064.1|CK052064
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
EST: gi|66922614|gb|CX119142.1|CX119142
EST:     AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCT                         GTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG
genomic: AAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAG

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: 71 (upstream exon), 75 (downstream exon)
Score: 25

CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggattt ... ctttaaacagGTTAAACTTCTTTTTGCCGCGGAACGTCAGCTTTGTGACCAGGTTTTTGAGTGCAGTCAATCTTTGAGGGATAAGTGCTTTGCTCAAATAACTAGGAATA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG