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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctactacttatccttgtgtactgcctttcatccatgcgctcctatttgtggtgctcttgactgacttttatcatgtactgtgctacttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATATGCACGGTTCTTTGAAGAGCACACTCACAGGATATATGTACTATCCATAA

Basic information

species Oryza sativa
transcript LOC_Os02g55200.1
intron # 7
splice site 3'
intron type U2

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|89166002|gb|CI103092.1|CI103092
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|29657742|gb|CB654017.1|CB654017
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|89189931|gb|CI049470.1|CI049470
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACCAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|88829494|gb|CI074364.1|CI074364
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|87008607|gb|CI315065.1|CI315065
EST:     CCTTGAGAA-TTGAAGCCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: CCTTGAGAATTTGAAG-CTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|86259820|gb|CI065693.1|CI065693
EST:     CTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: CTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|88902604|gb|CI088142.1|CI088142
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTTTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|86597624|gb|CI274615.1|CI274615
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|88219081|gb|CI220354.1|CI220354
EST:     AAGCTGGAATCTGGAGAGCCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: AAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|86872668|gb|CI329622.1|CI329622
EST:     GAATTTGAAGCT-GAATCTGGAGAGGCCACTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGAAAA
genomic: GAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|58589478|gb|CF987786.1|CF987786
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|88990288|gb|CI107714.1|CI107714
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGCCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACGAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|16579745|gb|BI813840.1|BI813840
EST:     CTGGAATCTGGAGAGCCCAGTCTTGA-CAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACCAAAACAACTGGATGACAAGTGATAT
genomic: CTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|29659820|gb|CB656095.1|CB656095
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|88219655|gb|CI219215.1|CI219215
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|9865344|gb|AU101094.1|AU101094
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
EST: gi|86842452|gb|CI335325.1|CI335325
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCACCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATAT

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), 70 (downstream exon)
Score: 13

TCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAATGCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATATGCACGGTTCTTTGAAGAGCACACTCACAGGATATATGTACTATCCATAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctatttgtggtgctcttgactgacttttatcatgtactgtgctacttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATATGCACGGTTCTTTGAAGAGCACACTCACAGGATATATGTACTATCCATAA
                   gactgac  putative branch site (score: 13)
                                           ctactttt  putative PPT
                          ttttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctactacttatccttgtgtactgcctttcatccatgcgctcctatttgtggtgctcttgactgacttttatcatgtactgtgctacttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAACTGGATGACAAGTGATATGCACGGTTCTTTGAAGAGCACACTCACAGGATATATGTACTATCCATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA