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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataaaatttgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 21
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataaaatttg-cacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag
||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||| |   |   |||  | ||   ||   | | |||   ||   ||||   |||||    |  ||| ||   |||  ||| |||
AGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCATCCACATATACAATGTCAGGGTAGATGAGgtaatcagtgtctaatctctgatgcagtttatgattctgtggatcatt-tcattcagcctt-ctgacct---tttggttttcag

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G416836_T01 (Zea mays), 5'ss of exon 19
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataaaatttg-cacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag
||||||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||| || |||||| |||||||||||||| ||||  |  || | |||  | ||   ||   | |  ||   |||  ||||   |||||    |  ||| ||||    | |      
AGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCATTCACATATACGATGTCAGGGTAGATAAGgtgataaatgcctaatctatgatgcagtttatggttctgtgaatcatt-tcattcagcctt-ctgacctttggggtttcag---

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GLYMA19G41840.3 (Glycine max), 5'ss of exon 21
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataaaa----tttgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag-------
 || || |||||| | || || ||||||||||| || || |||||||| ||||| ||||| |||||||| || || ||||| ||||| || || ||||||||  |   ||  |  ||    |||   |||  |   ||||||   |  |||  | || |||| | |     ||| | ||   |  |        
TGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAATTCACATATATAATGTTAGAGTGGATGAGgtgattactatctttaactgtttttttcattttaagatttat---gttattatttttaatttgtctcatattttctcttgggtgtatattctag

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 22
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataaaat---ttgcacatactgtaatttattgagccattgctattcatttatattgagctttatttt-------ctttccag
 || || |||||| |||| || ||||||||||| ||||| |||||||| ||||| ||||| |||||||| || || ||||||||||| || || ||||||||  |   ||  |  | |   ||     |  | | ||||     || |||  | || |||| | |     ||| | ||         ||| ||
CGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAGgtgattactatctttactgcttttttttttttttcattttaaatgctattatttttaatttgtgtcatattttctcttgggggtatcttctag

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 5'ss of exon 21
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataa---aatttgca-catactgtaatttattga-gccattgct-attcatttat--attgagctt------tattttctttccag------
||| ||||| || || |||||||| |||||||| |||||||| || ||||| || ||||| || || |  || ||||| ||||| ||||||||||||||||||  | | |  |     | | |||    |||||   |||| ||  |  | |||| |||||| | |  | |||  ||      || | |||||  |       
AGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTATACATATTTACAACGTCAGGGTAGATGAGgtatagtacatttgttctattctgcggtctactggtttttactggtgtaactgctgattcatctcttaaatgaatttgtaatgtaatctcttttaatctatag

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgta-ctgcatacataaaatt-tgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag
 || ||||||||  |||| || || |||||||||||||| |||||||| || |||||||| ||||| |||||||| || ||||||||  ||||||||||||||  | |||  |||| ||| | ||  |  | | | |  ||     |   ||||| | | ||  |||  |||  |    ||| ||
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatg-ataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgc--ttctag

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata----------cataaaatttgcacatactgtaatttattgagccattgct-attcatttatattgagctttattttctttccag--------------------------------------
|||| | || ||| | |||||||| || |||||||| |||||||| || || |||||||||||||| || || || || || |||||  | || |||||||||    ||           || | || |||| | |  ||| |||| |    |   || | || ||| | | | | | |||| | |    |                                         
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgc-ttttgtgatttgtcacacttgtgttgatgcatatgtctcg-gttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag

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|86860682|gb|CI324949.1|CI324949
EST:     TATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|58694171|gb|CK082858.1|CK082858
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|29625565|gb|CB630576.1|CB630576
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|58680385|gb|CK069072.1|CK069072
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|58611343|gb|CK039055.1|CK039055
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|33795487|gb|CF323613.1|CF323613
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|88828342|gb|CI000451.1|CI000451
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|163927986|gb|EG712962.1|EG712962
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcatacataaaatttgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA