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

...atatctgaatttagttccttaatgaattttttgatgctttaattttctgctaccacatatttttgcaatataatttatttgttcattctgttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG

Basic information

species Oryza sativa
transcript LOC_Os04g40040.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
-----atatctgaattta-gttccttaatgaattttttgatgctttaattttctgctaccacatatttttgcaatataatttatttgttcattctgttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG
       ||   | | || |   |  || |     |  || |   ||||||||||   |  || | ||||| |||      |||||||| || || |||| |  ||||||| || ||||| ||||||||||| |||||||||||||| ||||| || ||  |||||||||||||||| || |||||||| ||||| ||||| ||||
gaatggaattcaattctaaggatccaaacggggactaagaggaaataattttctgaagcttcaaagttttgtaat------tatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 7
atatctgaatttagttccttaatgaattttttgatgctttaattttctgctaccacatatttttg---caatataattt-atttgttcattctgttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG
|   ||||||     |  || ||   |||| ||||  | || |||  |  | | | ||||||      |||||| |||| || | || | | | ||   | |||||||| || || ||||| ||||||||||||||||| || || ||||| |||||||||  ||| || ||| |  |||| || ||||| || ||||||||||
agtgctgaatccgagt--ttcatttgttttctgat-ttgtagtttcatctttctagatatttgaagaccaatatcattttatgtcttgaatgtcttac-tgtagGATGGGAAAATCGAAGCTGAAGTAAAACTTACTGGTATCCTCAGTTTAGGAGCTCTGCAGCCAGGTGAAACTCGAAAGTACGGTACTACTATTGCTCCTG
















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|86905761|gb|CI290895.1|CI290895
EST:     TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
EST: gi|29673126|gb|CB669401.1|CB669401
EST:     TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
EST: gi|25806973|gb|CA762934.1|CA762934
EST:     TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTCTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
EST: gi|11442746|gb|BF430649.1|BF430649
EST:     TCTGCACAGTTGCCAACTATGAATATGGGTTTTACTGGCACTTCTATCAG                         GATGGCAAGATAGAAGCAGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGA
EST: gi|58690279|gb|CK078966.1|CK078966
EST:     TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
EST: gi|58604335|gb|CK014863.1|CK014863
EST:     GGCACTTTTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: GGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
EST: gi|58682321|gb|CK071008.1|CK071008
EST:     TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
EST: gi|29665204|gb|CB661479.1|CB661479
EST:     TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAG                         GATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA
genomic: TCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGA

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: 73 (upstream exon), 75 (downstream exon)
Score: 30

AACTGGTTTAGCAGAAGTTAGGAGGTCAAGGAGGCTTACTGTTTCATTTATCTGCACAGTTGCCAACTATGAATATGGTTTTTACTGGCACTTTTATCAGgtaattgttt ... ttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgctaccacatatttttgcaatataatttatttgttcattctgttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG
                                        ttctgtt  CT-rich tract
           atatttttgcaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatctgaatttagttccttaatgaattttttgatgctttaattttctgctaccacatatttttgcaatataatttatttgttcattctgttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg