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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttcttccatcatacgtactgaaaataaaaatgagttaaacaaagtaatgtgcatatggatcattcctcatggatttatctgtgtccgtttggctcgtgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAATACCAAACAATCTGCAACATAG

Basic information

species Oryza sativa
transcript LOC_Os10g34750.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G071304_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------gtatgc-tttcttccatcatacgtactgaaaataaa--aatgagttaaacaaagtaatgtgcatatggatcattcctcatggatttatctgtgtcc-gtttggctcgtgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAATACCAAACAATCTGCAACATAG
                                                  || || ||||||||  | |   ||       |     |   |||||    || |  | |   | ||  || ||  ||    |   || | | | | ||     |  |||||||||||||| | ||||||||||||||| ||||| || |||||||||||||||||||| |||||||| ||||||||||
gtggatgattctttttctatcatgcttactgataaaaaatgaactaattttaagcgtttcttccccccttgatataactgcttgttcatcaagttatttcaattgcttta-gtttgtttcttttttcggtaaaccatgtttattctgtccttgttttgcttactagGTGTCTTTGGATCATTCCTCCTCGCATGCTATGATGAGCAGAACGAAGAATATCAAACAATATGCAACATAG
















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|3763423|gb|AU030175.1|AU030175
EST:     TTGGATTTGGTGCCAATTGCTGCCTTTCATGGGGAGAGGGAAACGTACAG                         GTGTATATGGGTCATTCCTCCTGGCATGTTACGATGAGCAGACCGANGAAT
genomic: TTGGATTTGGTGCCAATTGCTGCCTTTCATGGG-AGAGGAAAACGTACAGgtatgctttc ... tgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAAT
EST: gi|5803572|gb|AI978542.1|AI978542
EST:     TTTGGATTTGGTGCCAATTGCTGCCTTTCATGGGAGAGGAAAACGTACAG                         GTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAAT
genomic: TTTGGATTTGGTGCCAATTGCTGCCTTTCATGGGAGAGGAAAACGTACAGgtatgctttc ... tgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAAT
EST: gi|29629335|gb|CB634346.1|CB634346
EST:     TTTGGATTTGGTGCCAATTGCTGCCTTTCATGGGAGAGGAAAACGTACAG                         GTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAAT
genomic: TTTGGATTTGGTGCCAATTGCTGCCTTTCATGGGAGAGGAAAACGTACAGgtatgctttc ... tgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatggatcattcctcatggatttatctgtgtccgtttggctcgtgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAATACCAAACAATCTGCAACATAG
                     atttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttcttccatcatacgtactgaaaataaaaatgagttaaacaaagtaatgtgcatatggatcattcctcatggatttatctgtgtccgtttggctcgtgcttactagGTGTATATGGATCATTCCTCCTGGCATGTTACGATGAGCAGAACGAAGAATACCAAACAATCTGCAACATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA