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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATTCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccag

Basic information

species Oryza sativa
transcript LOC_Os01g08700.8
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G107101_T05 (Zea mays), 5'ss of exon 5
CTAATTCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccag-----
|| |||||||||| |||||||||||||||||| ||| | |||||||||||||| ||||||   | |   | ||  | |  |||    ||   || | |||||||| | | ||||||  || | |  |     |     
CTCATTCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaactccttatggacaattgt----caggaaactcaagaaagaatctaacatatcatttttaattgcattgtacag

upper sequence: LOC_Os01g08700.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 4
CTAATTCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccag-----
|| |||||||||| |||||||||||||||||  ||| |  ||||||||||||| ||||||   | |   | ||  |||  || |    |   |||| |||||||| | |||||  ||| | | |  |   | |     
CTCATTCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGGgtaatacaaacttcttatggataattgct----aggaaattcaagaaagaatctgacaagtttcttttacttgcactgtacag
















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|29667209|gb|CB663484.1|CB663484
EST:     GATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCNTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: GATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29636922|gb|CB641931.1|CB641931
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88369882|gb|CI680559.1|CI680559
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29646260|gb|CB651267.1|CB651267
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCNTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29636923|gb|CB641932.1|CB641932
EST:     ATCCATCAAAAGAAAAGCGCCTGGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: ATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88587781|gb|CI705554.1|CI705554
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88361618|gb|CI680183.1|CI680183
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88369175|gb|CI680281.1|CI680281
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|58590243|gb|CF988551.1|CF988551
EST:     CAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAGCGGTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: CAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29642016|gb|CB647023.1|CB647023
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88454127|gb|CI694894.1|CI694894
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAATTCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccag

- - - - - - - - - - - - AAAGAA
- - - - - - - - - - - -  AAGAAA