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

CTTGGCCAAGCCCCGGCGAGGCAAGCCGCCCTAGGCGCCGGCTTGCCCGACACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgctattttaacctctctctctctctctctctctctctctctctctttttcagttgttacttgtttctgctactcgaggatcggcttttgctttgctatctagtgctacttaaaaatgggtcttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g02020.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G860137_T01 (Zea mays), 5'ss of exon 3
CTTGGCCAAGCCCCGGCGAGGCAAGCCGCCCTAGGCGCCGGCTTGCCCGACACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttc-gctattttaacctctctctctctctctctctctctctctctctctttttcagttgttacttgtttctgctactcgaggat-cggcttttgctttgctatctagtgctacttaaaaatgggtcttgcag
|||||||| || ||||| ||||| || ||||| ||||||||||||||| || | ||||| || |||||||||||||||||||| |||||||| |||||||||  |  |  ||| |   |      | | | | |   |   |   |   |  | ||   |||||  || || |     ||  |  | |     |   ||  ||| |                               
CTTGGCCAGGCTCCGGCAAGGCAGGCAGCCCTTGGCGCCGGCTTGCCCAACTCCGTGCCATGTACCACCGTCAACAAAGTTTGTTCCTCGGGAATGAAGGgtgctcgctactactaccaatatattttgtatattgattgattgttgattagccttgcaagttgcaacctgatagccttatcctggaacgttaccactgacttgttgcag---------------------------
















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|88377671|gb|CI605506.1|CI605506
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|117240405|gb|CT842781.1|CT842781
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|29641199|gb|CB646206.1|CB646206
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|58588269|gb|CF986577.1|CF986577
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|88360863|gb|CI625169.1|CI625169
EST:     ACTGTGCCCTGCACCACCGTCAACAAACGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCCTTGCGGCGCA
genomic: ACTGTGCCCTGCACCACCGTCAACAAA-GTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGC-TTGCGGCGCA
EST: gi|29675316|gb|CB671591.1|CB671591
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|33804994|gb|CF328374.1|CF328374
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|568197|gb|D39032.1|D39032
EST:     GTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: GTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|58590983|gb|CF989291.1|CF989291
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|88411332|gb|CI564453.1|CI564453
EST:     CACTGTGCCCTGCACCAC-GTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|29640750|gb|CB645757.1|CB645757
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|427922|gb|D24066.1|D24066
EST:     GTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: GTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|88389914|gb|CI626683.1|CI626683
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGC
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGC
EST: gi|58654730|gb|CK043410.1|CK043410
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTGGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
EST: gi|88392592|gb|CI625414.1|CI625414
EST:     ACTGTGCCCTGCCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGA
genomic: ACTGTGCCCTGC-ACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGA
EST: gi|58608101|gb|CK036134.1|CK036134
EST:     CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGG                         CTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG
genomic: CACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgc ... ggtcttgcagCTGTCATGCTTGCGGCGCAGACTATTCAGCTTGGGATGCATGATGTTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGCCAAGCCCCGGCGAGGCAAGCCGCCCTAGGCGCCGGCTTGCCCGACACTGTGCCCTGCACCACCGTCAACAAAGTTTGCTCCTCGGGGATGAAGGgtaatttcgctattttaacctctctctctctctctctctctctctctctctctttttcagttgttacttgtttctgctactcgaggatcggcttttgctttgctatctagtgctacttaaaaatgggtcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC