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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGAACCAAAGCACACCATCAGCAACCGCTGCTCCTGGGTTTGATGGAACAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactaccatggcacttaaatttgtacaagcatgaattcaatagcaatctaacttccgtaaatttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g50480.1
intron # 9
splice site 5'
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|218484613|gb|FG968698.1|FG968698
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|30229090|gb|CB966981.1|CB966981
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|66926016|gb|CX112864.1|CX112864
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGA
EST: gi|86854599|gb|CI258892.1|CI258892
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|58691641|gb|CK080328.1|CK080328
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|38481285|gb|CF965374.1|CF965374
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|38475530|gb|CF959663.1|CF959663
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTGGGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|33801990|gb|CF326868.1|CF326868
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
EST: gi|218498351|gb|FG945080.1|FG945080
EST:     CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAG                         AGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA
genomic: CAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCA

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: 70 (upstream exon), 58 (downstream exon)
Score: 26

CCTGAACCAAAGCACACCATCAGCAACCGCTGCTCCTGGGTTTGATGGAACAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactacca ... tttcttgcagAGCGAGAACGCTGCGATGTGGATGCATGGTGCCAGTTCGCGAACAATGCCACCTCTTGCAGCAAATGCCTTGTATTATCAAGGGCAGCAGGGTCACCAGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGAACCAAAGCACACCATCAGCAACCGCTGCTCCTGGGTTTGATGGAACAGTGCCCGCGCAATACAAAGAAGGGAATCAATTTGTATCTCTTCAGCAGgtaactaccatggcacttaaatttgtacaagcatgaattcaatagcaatctaacttccgtaaatttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG