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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGTGGACACCAGATGAAATTAAAGCTGCTACTGGGAATGAAGATTGCACCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgctaacttcacatggctagctacaatttctccatcaatctttgatgtgagaaatcaacatgtttcaccactcatctttatttagatatatcaga...

Basic information

species Oryza sativa
transcript LOC_Os01g42490.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42490.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G034430_T01 (Zea mays), 5'ss of exon 12
CAGGTGGACACCAGATGAAATTAAAGCTGCTACTGGGAATGAAGATTGCACCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgctaacttcacatggctagctacaatttctccatcaatctttgatgtgagaaatcaacatgtttcaccactcatctttatttagatatatcaga-
   |||||||||||| ||||| |||||||| |||||||| || || ||||| ||| || |||| | ||||||| |  | ||||| || || || || |||||||   |    ||        ||  |   |    | ||    |    ||    || ||     | |  |  | |   |     |   | | | |  ||| 
---GTGGACACCAGAAGAAATCAAAGCTGCCACTGGGAAGGATGAATGCACTTTCATGAAACACAGTTTGAAATTAAGGAGTGTATATACTGACGTCGAGgtaagtacgtcttttttccttttattttgtacgcatacagtggtggaggacaaaaggaaa-gggaggcatggctagctagaagaaaaaaaagaaaaaagag
















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|157650229|gb|EX449863.1|EX449863
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|86480117|gb|CI122750.1|CI122750
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|87027334|gb|CI270009.1|CI270009
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|29624406|gb|CB629417.1|CB629417
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|86858239|gb|CI271125.1|CI271125
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|2800930|gb|AA754224.1|AA754224
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|29624470|gb|CB629481.1|CB629481
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|87013807|gb|CI271198.1|CI271198
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|58690956|gb|CK079643.1|CK079643
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|29624531|gb|CB629542.1|CB629542
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|58677956|gb|CK066643.1|CK066643
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|86480856|gb|CI123489.1|CI123489
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|29635013|gb|CB640022.1|CB640022
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
EST: gi|29637193|gb|CB642202.1|CB642202
EST:     CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAG                         GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC
genomic: CCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgcta ... gttcaaccagGATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGTGGACACCAGATGAAATTAAAGCTGCTACTGGGAATGAAGATTGCACCTTCGTGGAACATAATTTGAAAGTCCGAAGTGTCTACACAGATGTGGAGgtaaccgctaacttcacatggctagctacaatttctccatcaatctttgatgtgagaaatcaacatgtttcaccactcatctttatttagatatatcaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG