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

...acgttatagattgatgtcaacttctaggtttaccttctgcttgctgcttttataggtttacaaccaacacgtagtcttagtgtgttatttatttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g10280.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g10280.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G701058_T01 (Zea mays), 3'ss of exon 14
acgttatagattgatgtcaacttctaggtttaccttctgcttgctgctt--ttataggtttacaaccaacacgta-gtcttagtgtgttatttat-ttgtg-cagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG---------------------------
|| | | | | | | | || | || | || |||||| |||| | | ||| || || || | | ||| |||| | ||||| ||||||| || |||||||| || || || || ||||||||||||||||||||||| ||||||||||||||||||||
---ttctgggattacggtaccccctt--tctatgtcgatgtttctgcttggttatctggtcacactcagcatttacatagcactgttccatttttcttgtgacagTGGGTCTCTACCTGCACCTCGCTGTGTCGGTTGTGCATGAAATCAAGGATGCCCTTGGAATCTATTGCTTCAGGTGTGGAAACTGGAAACCTCCGTGTGC

upper sequence: LOC_Os06g10280.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G701058_T02 (Zea mays), 3'ss of exon 3
acgttatagattgatgtcaacttctaggtttaccttctgcttgctgctt--ttataggtttacaaccaacacgta-gtcttagtgtgttatttat-ttgtg-cagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG
|| | | | | | | | || | || | || |||||| |||| | | ||| || || || | | ||| |||| | ||||| ||||||| || |||||||| || || || || ||||||||||||||||||||||| ||||||||||||||||||||
---ttctgggattacggtaccccctt--tctatgtcgatgtttctgcttggttatctggtcacactcagcatttacatagcactgttccatttttcttgtgacagTGGGTCTCTACCTGCACCTCGCTGTGTCGGTTGTGCATGAAATCAAGGATGCCCTTGGAATCTATTGCTTCAG
















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|88536305|gb|CI466049.1|CI466049
EST:     TATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: TATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
EST: gi|88265983|gb|CI376885.1|CI376885
EST:     TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
EST: gi|86861509|gb|CI328196.1|CI328196
EST:     AGTTAATGAGCTCCTGGTTCTTTTCCTGTATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: AGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
EST: gi|86435856|gb|CI107089.1|CI107089
EST:     TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
EST: gi|86536568|gb|CI176774.1|CI176774
EST:     TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
EST: gi|86869993|gb|CI317914.1|CI317914
EST:     TCCTTTATTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCGTACACAG                         -GGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
EST: gi|88524956|gb|CI453573.1|CI453573
EST:     GTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCC-TNTTCTGTTGTGCATGAAATCAAGGAT
genomic: GTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGT-TTCTGTTGTGCATGAAATCAAGGAT
EST: gi|38483180|gb|CF966982.1|CF966982
EST:     TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAG                         TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG
genomic: TCCTTTAGTTGATGAGCTGCTGGTTCTTTTCCTGTATTGCGCATACACAGgtgaactgat ... atttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttataggtttacaaccaacacgtagtcttagtgtgttatttatttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG
                                          tttattt  CT-rich tract
 tgtgttatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgttatagattgatgtcaacttctaggtttaccttctgcttgctgcttttataggtttacaaccaacacgtagtcttagtgtgttatttatttgtgcagTGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - ttgatgt
- - - - - - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtta