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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATTAGCTACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatag

Basic information

species Oryza sativa
transcript LOC_Os05g04340.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 4
ACCATTAGCTACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgt---tctggtggcgattgatgaacccttcatttctt-------------gaatgatcttgtatag
|||||||| |||||||| ||||| || ||||||||||| ||||| ||||| |||||||||||||||   || ||| |||  | |       | || |   || | |    | || | |   |  ||| |  | | ||    |||||   ||||              |||||||||||| ||
ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttactatacaaatcagtatgaaactgaattatctggtttttattgtagtatttcacttaggtagtaactaatagctccttcccctctttttttataaaaataaatgatcttgtacag
















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|12622374|gb|AU172587.1|AU172587
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29628929|gb|CB633940.1|CB633940
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAT
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|88298568|gb|CI563563.1|CI563563
EST:     CATGGCCGAGCCGTGTCGTANGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGGAGACTGGTGGCTATAAAGAAGGTTCTTT
genomic: CATGGCCGAGC-GTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTG-AGACTG-TGGCTATAAAGAAGGTTCTT-
EST: gi|58601571|gb|CK012099.1|CK012099
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGC
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGC
EST: gi|58663289|gb|CK051975.1|CK051975
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|33658344|gb|CF280957.1|CF280957
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29630931|gb|CB635940.1|CB635940
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|58603162|gb|CK013690.1|CK013690
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29626488|gb|CB631499.1|CB631499
EST:     CATGGGCC-AGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: CATGG-CCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29629558|gb|CB634567.1|CB634567
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|25798115|gb|CA754076.1|CA754076
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|58598716|gb|CK009244.1|CK009244
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATTAGCTACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatag

- - - - - - - - - - - - - - - -  CATGGA