Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGAGCACCCGGCCAAGAGCGACGGGTCGCTGAGCCTGCTCGTCGTCGGCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaaacgccccctcctcctccgtcggccgcgatccgtttcctcgcttcccgggatttaactctagttgttaaattttgctctaattgctgcggt...

Basic information

species Oryza sativa
transcript LOC_Os03g13540.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13540.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G152477_T02 (Zea mays), 5'ss of exon 1
GGTGGAGCACCCGGCCAAGAGCGACGGGTCGCTGAGCCTGCTCGTCGTCGGCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaa--aacc------aaacgccccctcctcctccgt--cggccgcga-tccgtttcctcgcttcccgggatttaactctagttgttaaattttgctctaattgctgcggt
| ||||||||||| |||||  || ||| ||||| ||||||||||||||||||||||||||||| |||||||||| |||||| |||||||||||| | ||||||   ||||      ||||  | |  |  | | |||   | ||  || |||| ||||     ||  |  || |    |  | || |   ||   |    |          
GCTGGAGCACCCGCCCAAGGACGGCGGCTCGCTCAGCCTGCTCGTCGTCGGCGACTGGGGCCGAAAGGGCACGTTCAACCAGTCCAGGGTCGCCCATCAGgtacgtaaccgccgttaaacaacacaactacgtacgtactgcccaagaatccgcttccc--tctcttgatatcttggccacggtggtggtttcaccgacgac---------
















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|86897826|gb|CI289048.1|CI289048
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|58656595|gb|CK045275.1|CK045275
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGTGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88397991|gb|CI585494.1|CI585494
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88391216|gb|CI595470.1|CI595470
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|87023940|gb|CI288293.1|CI288293
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGNGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88300996|gb|CI592176.1|CI592176
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|58593522|gb|CF991830.1|CF991830
EST:     CGACTGGGGCCGGAAGGGCACGTACAACCAATGGC-GGGTCGCCGAGCAG                         ATNGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: CGACTGGGGCCGGAAGGGCACGTACAACCAAT-CCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88576672|gb|CI670817.1|CI670817
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|58587652|gb|CF985960.1|CF985960
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88724631|gb|CI747890.1|CI747890
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88310928|gb|CI659531.1|CI659531
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88689485|gb|CI733061.1|CI733061
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88735033|gb|CI758541.1|CI758541
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88398672|gb|CI598637.1|CI598637
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88378503|gb|CI636450.1|CI636450
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|11026112|gb|AU162713.1|AU162713
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|58685580|gb|CK074267.1|CK074267
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|88296190|gb|CI667580.1|CI667580
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|117234872|gb|CT847928.1|CT847928
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|58659633|gb|CK048313.1|CK048313
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|58608007|gb|CK036040.1|CK036040
EST:     CGACTGGGGCCGGAAGGGCACGTACAACCAATCCANGGG-CGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: CGACTGGGGCCGGAAGGGCACGTACAACCAATCCA-GGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|87009731|gb|CI310834.1|CI310834
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
EST: gi|25797391|gb|CA753352.1|CA753352
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATGGGGAAGGTTGGGGAGA
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGA
EST: gi|5900737|gb|AU078392.1|AU078392
EST:     GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAG                         ATNGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT
genomic: GCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGT

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: 69 (upstream exon), 69 (downstream exon)
Score: 57

GGTGGAGCACCCGGCCAAGAGCGACGGGTCGCTGAGCCTGCTCGTCGTCGGCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaa ... tatcatgcagATGGGGAAGGTTGGGGAGAAGCTAAATATAGACTTCGTCATATCCACCGGTGACAATTTCTACGAGGATGGACTCACTGGCGTCGATGACCAGGCGTTTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGAGCACCCGGCCAAGAGCGACGGGTCGCTGAGCCTGCTCGTCGTCGGCGACTGGGGCCGGAAGGGCACGTACAACCAATCCAGGGTCGCCGAGCAGgtaaaaccaaacgccccctcctcctccgtcggccgcgatccgtttcctcgcttcccgggatttaactctagttgttaaattttgctctaattgctgcggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggccgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcgg