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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccttaataggtgacttttttggccagacataagtattttggccggtccgtaatagctaactagaataatatggttcttttttttaaaattccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTGCACTTGGTGCTGCACGTGCTCTTGCTTATTTGCATGAAGATTCTAGTCC

Basic information

species Oryza sativa
transcript LOC_Os01g51290.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 5
--ctccttaataggtgacttttttggccagacataagtattttggccggtccgtaatagctaactagaataatatggttcttttttt-taaaattccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTGCACTTGGTGCTGCACGTGCTCTTGCTTATTTGCATGAAGATTCTAGTCC
   |   || ||  |   | ||    | |    ||  ||  ||||  | | |   |||  |   | ||    |    |  | | ||  ||  |||| |||||||||||||||||||| ||||||   |||||||| | |||||||| ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| |||||
ggttgtgtagtatata--tcttcaatctacttttagttaccttggttg-tacactatatttttttggacatctgaaatcgtatattaatacgattctaagcagGATCAGATAAGGGAGCTGCTCAGTTTGATTGGAACGCTAGGCTCAAAATTGCACTTGGTGCAGCACGCGCACTTGCATATTTGCATGAGGATTCAAGTCC

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 4
-ctccttaataggtgacttttttggccagacataagtattttggccggtccgtaatagctaactaga-at---aatatggttcttttttttaaaattccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTGCACTTGGTGCTGCACGTGCTCTTGCTTATTTGCATGAAGATTCTAGTCC
  || |   |  |     | | |   ||  |     || | |  |  || |   |||  |   | || ||   ||   | || || || | |  |||| || ||||||||||||||||| | ||||   |||| ||||| |||||||| ||||| ||||| ||||| |||||||  ||||| ||||||||||||||||| || ||
gttcatgtttgtgcagtatatatcttcaatc-----tactctcacttgtacactatattttcttggacatctgaaaccgattgttattatgatgattctaaacagGATCAGATAAGGGAGCCGCTCGGTTTGACTGGGACGCTAGGCTCAAAATCGCACTAGGTGCAGCACGTGGACTTGCATATTTGCATGAAGATTCAAGCCC
















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|29671018|gb|CB667293.1|CB667293
EST:     TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACG                         GATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
genomic: TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACGgtaatatttt ... ttccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
EST: gi|58665758|gb|CK054444.1|CK054444
EST:     TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACG                         GATCAGATAAGGGAACTGCTCCACTTTATTGGGATGCTAGGCTTAAAATTG
genomic: TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACGgtaatatttt ... ttccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
EST: gi|29673710|gb|CB669985.1|CB669985
EST:     TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACG                         GATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
genomic: TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACGgtaatatttt ... ttccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
EST: gi|29671060|gb|CB667335.1|CB667335
EST:     TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACG                         GATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
genomic: TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACGgtaatatttt ... ttccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG
EST: gi|29667620|gb|CB663895.1|CB663895
EST:     TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACG                         GATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTATAATTG
genomic: TCTTGTGTATGAGCTTGTTCCAAATGGTAGTGTGGAATCTCACTTGCACGgtaatatttt ... ttccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtccgtaatagctaactagaataatatggttcttttttttaaaattccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTGCACTTGGTGCTGCACGTGCTCTTGCTTATTTGCATGAAGATTCTAGTCC
          agctaac  putative branch site (score: 2)
             taactagaataatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccttaataggtgacttttttggccagacataagtattttggccggtccgtaatagctaactagaataatatggttcttttttttaaaattccaagcagGATCAGATAAGGGAACTGCTCCACTTGATTGGGATGCTAGGCTTAAAATTGCACTTGGTGCTGCACGTGCTCTTGCTTATTTGCATGAAGATTCTAGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA