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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcatattgtctttatgaaaagcttacttttgtagaattttttttaaaaagaatttcttttatttctgtag

Basic information

species Oryza sativa
transcript LOC_Os04g14654.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g14654.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G003734_T01 (Zea mays), 5'ss of exon 20
GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcatattgtctttatgaaaagcttacttttgtagaattttttttaaaa-----agaatttcttttatttctgtag
||| |||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||  |  | |   ||      |  ||   |||   | |        ||||     | |  || | | | || | |||
GCGGTCTATTGAAGAACTGTTGAAACTATTGCCAGGCCCACATCTGGATTTGAAAAGAgtgagtagagttcg---ttgaattgactttgtgttttagggaagcaaaaaaaaatccttacagattttctcacttatatag
















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|86599219|gb|CI355836.1|CI355836
EST:     CCAGGTCCTCATCTGGATTTGAAAAGA                         GGTAGTTC-GCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
genomic: CCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
EST: gi|58603195|gb|CK013723.1|CK013723
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGA                         GGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
EST: gi|163917728|gb|EG711274.1|EG711274
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGA                         GGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
EST: gi|88273383|gb|CI393789.1|CI393789
EST:     GAAGAAGCTG-TGAAACTATTGCCCAGGTCCTCATCTGGA-TTGAAAAGA                         GGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
genomic: GAAGAA-CTGTTGAAACTATTG-CCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
EST: gi|28298184|gb|CB238414.1|CB238414
EST:     TTGGAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGA                         GGTAGTTCGGCCATTA
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTA
EST: gi|88250349|gb|CI348579.1|CI348579
EST:     TGAAGAACTGGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGA                         GGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
genomic: TGAAGAACT-GTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
EST: gi|86432914|gb|CI093257.1|CI093257
EST:     TTGAAGAACTGTTGAAACTATTGCCAGGTCCTTATCTGGATTTGAAAAGA                         GGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT
genomic: TTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcat ... atttctgtagGGTAGTTCGGCCATTAATTCTTCATTGGATGTACACCAAGGTTTGGGGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATCTATTGAAGAACTGTTGAAACTATTGCCAGGTCCTCATCTGGATTTGAAAAGAgtgagtgcatattgtctttatgaaaagcttacttttgtagaattttttttaaaaagaatttcttttatttctgtag

- - - - TTGAAG
- - - -  TGAAGA
- - - - -  AAGAAC