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

...aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g40830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 5
-aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttct-tgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
    || |||   | |    | | |  |  |   ||   ||      | |     || | |||  | ||  |  |  || | |  |  |  | ||||| ||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| || |||
gtcaaagtaacttaatgcaca-tcatcaatctcctttttctgaaatggttgtatattttatgaagttttttttaaccctcatttctgattgcccattt-cagCTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------aagaattaaaccattaggtagttaatatgcatgttcccctatttcag---ataggggttcttgactt--cttgctgtagac--taactgatt---ttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
                                                                       ||    |    |  |   |  || || | ||  |||    | || |    |||    || || |  |  |||  | ||     |  || |||   ||    | ||| ||| | || || || || || |||||||||||||| |||||||| ||||||||||| |  || || ||||| || |||
gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcat-tacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 5
-------aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagact---aactgattttcactcattt-tcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
       |  |   |||  || || | | |  ||| ||| |||||   ||  ||  | |   | || |   | |||||||   |   ||  | ||| |  || | | |||| | || || || || |  ||||| || |||||||||||||||||||| ||||||| |||||| ||||||||||||
gtatgctactacgcaaatgatgagct-gctgctattcat-ttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAGAAGTTCCCTGACATGATCATCAAG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 5
aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
         |   ||  ||  || |      | |      ||| ||  |     |      ||   |     |   | ||| |  |   ||  | | ||| |||| || || || || |||||||||||||| || ||||| ||||||||||| | |||||| |||||  |||||
gtcctgcccatatttgtgtgttttaccattttatcatgaaattacacttgaaaatatagatctaaatttaagatgtttactcacatattctgctctccagATCATAATTGCATGTAGAAAGGGAGGAACCAGCATCGAAGACCTTGCAGAGAAATTCCCTGACATGATTGTCAAG

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|163928461|gb|EG715441.1|EG715441
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCATCAAGGGAGGAACCATTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|66913068|gb|CX099916.1|CX099916
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|88361440|gb|CI605221.1|CI605221
EST:     AATGAGATGTACTTCGCCATCACCCTTGACAGGGAATACTGCTGGTCCCG                         CTCATTATAGCGTGCAGCAAGGGGAAGGAACCAGTATTTGAAGA
genomic: AATGAGATGTACTTCGCCATCACCCTTGACAGG-AATACTGCTGGTCC-Ggtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGG-A-GGAACCAGTATT-GAAGA
EST: gi|29662328|gb|CB658603.1|CB658603
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|4714828|gb|AU055945.1|AU055945
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|29662110|gb|CB658385.1|CB658385
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|38478366|gb|CF962499.1|CF962499
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|58684186|gb|CK072873.1|CK072873
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGA
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGA
EST: gi|13420568|gb|AU174658.1|AU174658
EST:     GAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: GAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|88730444|gb|CI754057.1|CI754057
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|33794775|gb|CF323267.1|CF323267
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
EST: gi|27577186|gb|CA999880.1|CA999880
EST:     TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG                         CTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG
genomic: TTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAG

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: 64 (upstream exon), 70 (downstream exon)
Score: 89

GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtcttt ... tcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG
                                      ttttcactcattttc  CT-rich tract
                                   tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaattaaaccattaggtagttaatatgcatgttcccctatttcagataggggttcttgacttcttgctgtagactaactgattttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - -aaaccat
- - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -gttcttg