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'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagaaagatatatttaagttcctttcgtgttactttacttcctgcaatatatatgttagtcacattcacacattgtgtcttattcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTGAAGCATATGAACTTGTTCGCCGTGGATTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g43030.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43030.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 2
gtatgcagaaagatatatttaagttcctttcgtgttactttacttcctgcaatatatatgttagtcacattcacacattgtgtcttattcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTGAAGCATATGAACTTGTTCGCCGTGGATTGAAG
|||||  ||| ||||| ||   ||||  ||    |||| | |  | |||   | |||    | || || | |   |  | ||||   || |  |||||||||  ||||||||||||||||||||||||| |||||||| || ||||||||||| || || |||||||| || ||  |||||
gtatgttgaaggatatgttctggttctatt---attacctca--tactgt--tgtattcacttgtaacttcc---ctctatgtcccgtttca-tgtagAAACACTATCAATGAAAGGTTTGACGCTAAACTGCATGGACCGAAAATCTGAAGCGTACGAGCTTGTTCGACGAGGCCTGAAG
















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|88591151|gb|CI708067.1|CI708067
EST:     TTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: TTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88304950|gb|CI671208.1|CI671208
EST:     TTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: TTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88313578|gb|CI671703.1|CI671703
EST:     TTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: TTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88729096|gb|CI752606.1|CI752606
EST:     GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTCCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGGTTTGACGCTAAATTGCATGGATCGGAAATCT
genomic: GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAA-GGTTTGACGCTAAATTGCATGGATCGGAAATCT
EST: gi|88728684|gb|CI752194.1|CI752194
EST:     GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88369611|gb|CI582806.1|CI582806
EST:     GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88577420|gb|CI674006.1|CI674006
EST:     TTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: TTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88696007|gb|CI739582.1|CI739582
EST:     GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88587117|gb|CI704845.1|CI704845
EST:     TTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: TTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|58664912|gb|CK053598.1|CK053598
EST:     GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCG                         AAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
genomic: GGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTG
EST: gi|88393900|gb|CI684164.1|CI684164
EST:     TTTTAAAGAAGTTCCCTGAGCATGGCG                         AANA-CTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCT
genomic: TTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAA-ACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCT

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), 67 (downstream exon)
Score: 19

AAATCCTATGAGACAAAGCAATATAAGAAGGGCCTGAAGGCAGCAGATTCCATTTTAAAGAAGTTCCCTGAGCATGGCGgtatgcagaa ... tcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTGAAGCATATGAACTTGTTCGCCGTGGATTGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgcaatatatatgttagtcacattcacacattgtgtcttattcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTGAAGCATATGAACTTGTTCGCCGTGGATTGAAG
                                     tgtcttattcccct  CT-rich tract
       aatatatatgttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagaaagatatatttaagttcctttcgtgttactttacttcctgcaatatatatgttagtcacattcacacattgtgtcttattcccctgtagAAACCTTATCAATGAAAGGTTTGACGCTAAATTGCATGGATCGGAAATCTGAAGCATATGAACTTGTTCGCCGTGGATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG