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

AGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaagctagaccacttaaagtcgtgtccaaatctttggtgtagccataaaaaaattagctttcgctaaatttgaatgaagatagctacacttttatgttagtctcatattctttactatttttttcctattctccag

Basic information

species Oryza sativa
transcript LOC_Os01g53880.7
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53880.7 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G057067_T02 (Zea mays), 5'ss of exon 5
---------------AGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaagctagaccacttaaagtcgtgtccaaatctttggtgtagccataaaaaaattagctttcgctaaatttgaatgaagatagctacacttttatgttagtctcatattctttactatttttttcctattctccag
                || ||||| |||||||||||||||||||||||| | ||||| || |||||| || |     ||||| |     | || |||| | | ||   |||     ||  ||  |  |  | || |  || | ||  ||||  |   |   |||   |     | ||  ||||| | | | |                             
ATGTGATCCCTGCAGTGTGTTTGTGTCAACTGCTAAAAGGCTGAGGGTTTTGAGGAGCTCGGAGCTTGCCAAAGGTTTGGTAGGC---ACAAGGCCACCTCAGgtgacgtctg---ctgcgg-atttcagttaacatgtttgatt--gctagctccaagctaagtatg----gccttcctgttaattttacag----------------------------

upper sequence: LOC_Os01g53880.7 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G057067_T01 (Zea mays), 5'ss of exon 5
AGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaagctagaccacttaaagtcgtgtccaaatctttggtgtagccataaaaaaattagctttcgctaaatttgaatgaagatagctacacttttatgttagtctcatattctttactatttttttcctattctccag
 || ||||| |||||||||||||||||||||||| | ||||| || |||||| || |     ||||| |     | || |||| | | ||   |||     ||  ||  |  |  | || |  || | ||  ||||  |   |   |||   |     | ||  ||||| | | | |                             
TGTGTTTGTGTCAACTGCTAAAAGGCTGAGGGTTTTGAGGAGCTCGGAGCTTGCCAAAGGTTTGGTAGGC---ACAAGGCCACCTCAGgtgacgtctg---ctgcgg-atttcagttaacatgtttgatt--gctagctccaagctaagtatg----gccttcctgttaattttacag----------------------------
















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|86431330|gb|CI084941.1|CI084941
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCNGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|15857837|gb|BI810649.1|BI810649
EST:     TGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCA-TTGCTGA
genomic: TGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|86254278|gb|CI059005.1|CI059005
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|33655777|gb|CF278391.1|CF278391
EST:     AAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: AAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|86431162|gb|CI083585.1|CI083585
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|88269311|gb|CI380609.1|CI380609
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAAATTGCTG
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACC-AATTGCTG
EST: gi|4714720|gb|AU055837.1|AU055837
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGCGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTNGGGTCTAGCCGTCTAGGAGAGTCNCCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|88908179|gb|CI090774.1|CI090774
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|88227853|gb|CI227333.1|CI227333
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|88271388|gb|CI387441.1|CI387441
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|88274057|gb|CI394463.1|CI394463
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         AGTTGGAGCTACTGGTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTG
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagA-TTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTG
EST: gi|25798457|gb|CA754418.1|CA754418
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|13420516|gb|AU174606.1|AU174606
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|33655773|gb|CF278387.1|CF278387
EST:     AAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: AAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|58696125|gb|CK084812.1|CK084812
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|86884571|gb|CI312950.1|CI312950
EST:     CTGCTAAAAGGCTGA-GGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|18387819|gb|BM421017.1|BM421017
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
EST: gi|88289513|gb|CI555875.1|CI555875
EST:     CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTG                         ATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA
genomic: CTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaag ... tattctccagATTGGAGCTACTGCTAGGGTCTAGCCGTCTAGGAGAGTCACCAATTGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGgtaagacaagctagaccacttaaagtcgtgtccaaatctttggtgtagccataaaaaaattagctttcgctaaatttgaatgaagatagctacacttttatgttagtctcatattctttactatttttttcctattctccag

- - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - GAGCTT