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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactatctcttcattttcctccttctaggtcttactgaatagcagctagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA

Basic information

species Oryza sativa
transcript LOC_Os01g16290.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 10
---tcactatctcttcattttcctccttctaggtcttactgaatagcagctagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA
   | || || || | || |||    ||| ||   ||| |   |  |  | ||  |  | ||||||||    ||||||| ||  ||||  |  | |||||||||| ||||||||| ||||||||||| ||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| || ||| |||||||||| 
gttttacaat-tcgttatattctg--ttccagtgtttattatttgactacgagggaataattttgtgctcccttctgaagcaataaattgtccccatttacagGTCCTCTGATTCCTACTCTGATACAGTGCTAGGATACGCAAACAGTATCCGCACTATTGATGGTGGTACTCATATTGATGGTCTAAAGGCTTCATTGACG

upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA19G31030.1 (Glycine max), 3'ss of exon 10
-tcactatctcttcattttcctccttctaggtcttac-tgaatagcagctagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttac-agGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA
   |  | |  |  | ||   |  ||    || | |  ||  |  || |||   | ||   ||     ||| | ||  |   |     ||   | ||||| ||||     ||| |||| || |||||  | || ||||||||||| ||||| || |||||||||||||| |||||||||||||   ||||| ||||  | |||
aaaatgaacaatggaattgtatattttcctgtataatatggttgacaactattgataa---ttccattttagtttgtgattcatttcattgcttctttaccagGTCTGAAGATGCATATTCAGATACAATACTGGGATATGCTAATAGTATACGCACTATTGATGGTGGCACTCATATTGATGCTATGAAGGCTTCTATAACA

upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 10
tcactatctcttcattttcctccttctaggtcttac-tgaatagcagctagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttac-agGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA
  |  | |  |  | ||   |  || |  || | |  ||  |  || |||   | || ||   |       | ||  |   |     |||  | ||||| |||||    ||| |||| || |||||  | || ||||||||||| ||||| || ||||||||||||||||||||||||||||   ||||| ||||  | |||
-aatgaacaatggaattgtatatttttcagtataatatggctgacaactattcataa-ttccttattagtatatgtgattcatttcatttcttctttaccagGTGTGAAGATGCATATTCAGATACAATACTGGGATATGCTAATAGTATACGCACTATTGATGGTGGTACTCATATTGATGCTATGAAGGCTTCTATAACA

upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 10
-tcact-atctcttcattttcctccttctaggtcttactgaatagcagc-tagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA
  ||   |  | || | |       |  ||      |||||  | |  | | ||    |   |||      ||| |        |    |||| ||||   |||||||| ||| |||| || |||||  |||| ||||||||||| || || || || |||||||| ||||||||||| |||||  ||||| |||| ||||||
tgcatggaaatatttaatacaactatcatactcaaaactgacaaccttccttgactagaccattgaattgaattttcttgttttatgcatttgttatt---agGTGCTCAGATGCATATTCAGATACTATGCTGGGATATGCTAATAGCATACGCACAATTGATGGGGGTACTCATATCGATGGTATGAAGGCTTCTTTGACA

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|33677997|gb|CF306236.1|CF306236
EST:     GCATTCAGAAAAGAAATGGATGGAATAACAGTGGATGTTTCCCTTCAATG                         GTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCG
genomic: GCATTCAGAAAAGAAATGGATGGAATAACAGTGGATGTTTCCCTTCAATGgtaaaatgta ... ctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCG
EST: gi|58688095|gb|CK076782.1|CK076782
EST:     GCATTCAGAAAAGAAATGGATGGAATAACAGTGGATGTTTCCCTTCAATG                         GTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCG
genomic: GCATTCAGAAAAGAAATGGATGGAATAACAGTGGATGTTTCCCTTCAATGgtaaaatgta ... ctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA
                                   aaaatgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactatctcttcattttcctccttctaggtcttactgaatagcagctagatagaagttttgtgccttattctgaaacagaaaatgtttgctatttacagGTGCTCTGATTCATACTCTGATACGGTGCTAGGATATGCTAACAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA