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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtttcaacgcttctgtaccactttaaacattcttgctctcaagataagtacatgtaattcatctcattctctaccttattcag

Basic information

species Oryza sativa
transcript LOC_Os08g27030.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctg-tagt-ttcaacgct--tctgtac----cactttaaacattctt-gctctcaagataagtacatgtaattcatctcattctctaccttattcag
 |||| ||||||||||||||||| || ||||||||||| || ||||| ||||| |||||||||||||||||||||||||| ||||| |||||||| |||||| || |||| ||  | |||  | ||||     || ||  ||||  |||  |  |||| |      |||| | |   ||    |||      | |||||
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagt--gtcattctcttatttcttttcag

upper sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G18450.2 (Glycine max), 5'ss of exon 6
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtttcaacgcttctgtaccactttaaacattcttgctctcaagataagtacatgtaattcatctcattctctaccttattcag
 | || ||  | || || ||||| ||| |  |  | || |||||||| ||||| ||||| |||||||| ||||||||||| ||| | || ||  |||||||||||| |    |  |  | |       || |   |||  |  | | || |||  |   |  |   | | | || |      |||| |||
ATTGTTTTCTTTCCGCTTCTTGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTTTTTACTGGAGGGCTTATAGgtctgttgaag-actggattttctttgtttgatttattaata-tgtaaatatacttttctccaga-ctttttatacgagcttttatgcag

upper sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G25650.1 (Glycine max), 5'ss of exon 6
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtttcaacgcttctgtaccactttaaacattcttgctctcaagataagtacatgtaattcatctcattctctaccttattcag
|| || ||  | ||  | || || ||| |  |  | || |||||||| ||||| |||||||||||||| ||||||||||| ||||| || |   |||||||| |||  |  | | ||     |     | ||          | ||   || ||||   ||  |   || || ||  | |          
CTTGTTTTCTTACCAATCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTACTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTTATAGgtttgtt-tcccgaagccagattgattatatatttcaataaacccttttgaaaagtttctgatacgaatgtcttttaccag---------

upper sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G41580.1 (Glycine max), 5'ss of exon 6
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtttcaacgcttctgtaccactttaaacattcttgctctcaagataagtacatgtaattcatctcattctctaccttattcag
|| || ||  | ||  | || || ||| |  |  | || |||||||| ||||| ||||| |||||||| ||||||||||| ||||| || |   | ||||||   |||||| |  | | |   |    || ||| |||       | ||      |  | ||   | ||   | | | |   |||  |||
CTTGTTTTCTTACCATTCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTAATAGgt---tagttt-actgatgccagattgatt-aaatatttcaa---taaacccttttcaaagtttctgatacgaatattttttttac-cag

upper sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 5'ss of exon 5
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtttcaacgcttctg--taccactttaaacattc-ttgctct-------caagataagtacatgtaattca-tctcattctcta-ccttattcag------
 | || || |||||  ||||| ||||| | || |||| ||| ||||| || || || || |||||||||||||||||||||||||| || ||  | ||||||||||  | |||   |   ||  ||  | |  || | ||| || ||||          |||   ||||      ||| | | ||||| |  ||||  ||        
ATTGTTTTCCTGCCCATACTTCTTGCAGCTCTAGTGGGAGTTTCTCGAGTAGATGACTATTGGCATCACTGGCAAGATGTATTTGCCGGAGGTGTAATAGgtctgttttatcagtaccgatgattatgaatggaatctttccttactctacttttttctgatttatacactcttctcagtataattctttgtccttcctctctggcag

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|86525481|gb|CI165687.1|CI165687
EST:     CATCACTGGCAAGATGTATTTGCAGGCGGCATTATAG                         GTCTCACAGTTGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTG
genomic: CATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtt ... ccttattcagGTCTCACAGTTGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTG
EST: gi|86870409|gb|CI320505.1|CI320505
EST:     ACTGGCAAGATGTATTCCCAGCCGCCATTATAG                         GTCTCACAGTTGCTTCGTTTTGTTACCTCCAATTTTTCCCATATCCATTTG
genomic: ACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtt ... ccttattcagGTCTCACAGTTGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTG
EST: gi|33654798|gb|CF277412.1|CF277412
EST:     TGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAG                         GTCTCACAGTTGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTG
genomic: TGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtt ... ccttattcagGTCTCACAGTTGCTTCGTTTTGTTACCTGCAATTTTTCCCATATCCATTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctgtagtttcaacgcttctgtaccactttaaacattcttgctctcaagataagtacatgtaattcatctcattctctaccttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG