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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattggaagtgttttctagagtatcttggtatgatgaatacatatgttacaaaataactacataagcaatactacctctatatttatatatatgaca...

Basic information

species Oryza sativa
transcript LOC_Os10g36780.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36780.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G082502_T01 (Zea mays), 5'ss of exon 12
TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattg----gaagtgttttctagagtatcttggtatgatgaatacatatgttacaaaataactacataagcaatactacctctatatttatatatatgaca
|||| || |||||||| ||||| ||||| ||||||||||| ||||||||||| || || || ||    ||||||||||| |||||||  | |    |||  |   |  |  ||  | |       ||  |||    |      ||||   || |  |  |      |  || |   || |   |    
TGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGAGGGGCTGTCCGCAGTGGCCTTTCAGGATCGAAGgtaattcgaaacgaaaagaaataaacggttccataaagctttgc-tacgatcgcagtgcaatactgaccttggtcaccgggtcaatacaccaatctgcttt---
















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|88511365|gb|CI438871.1|CI438871
EST:     ACATGGCGCTGATGTGAGGGGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGGTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|88198073|gb|CI197923.1|CI197923
EST:     ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|157649959|gb|EX449593.1|EX449593
EST:     ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|88263249|gb|CI367023.1|CI367023
EST:     ACATGGCACTGATCTGAGAGGATTCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|86904683|gb|CI321591.1|CI321591
EST:     ACAT-GCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|88968629|gb|CI098843.1|CI098843
EST:     ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|88511080|gb|CI438586.1|CI438586
EST:     ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
EST: gi|88519380|gb|CI447034.1|CI447034
EST:     ACATGGCACTGATCTGAGANGATGCCCCCAACTCCCTTTCAGGATTGAAG                         GTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC
genomic: ACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattgga ... gcattatcagGTGACCCTTCAAATTGCTCATCCCCGGCAGCCGTGAGCACAGTGAGGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCATCATACATAATCAAATGTAGAAATTGCGGACATGGCACTGATCTGAGAGGATGCCCCCAACTCCCTTTCAGGATTGAAGgtagattggaagtgttttctagagtatcttggtatgatgaatacatatgttacaaaataactacataagcaatactacctctatatttatatatatgaca

- - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG