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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actattacaattcaaaatactagcacatgcatacttttctgggtaatcacttaattgatgatcctatatgctctatcgatatcttgttctgctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTCTGAGGTCTTGTTGCAGTGCTCCACCTCTCCAGCTGCCGAGCCACCACAT

Basic information

species Oryza sativa
transcript LOC_Os06g41390.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g41390.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G144362_T02 (Zea mays), 3'ss of exon 7
--------actattacaattcaaaatactagcacatgcatacttttctgggtaatcacttaattgatgatcctatatgctctatcgatatcttgttctgctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTCTGAGGTCTTGTTGCAGTGCTCCACCTCTCCAGCTGCCGAGCCACCACAT
         |   |   || |||   ||| | | |    ||| |  || | |          ||     | | |||   || ||||    | ||||        |||||||||| |||||||| || || || || ||||| |||||||| |||||||| || ||| || ||| |||||||||||||||||| || || ||||| || 
gtttaagagcgcatggtatccaacggactcggaaaca-gtacatgccttgtttgcttacagttttcccttaccataaaatccatcg----cctgttga---tacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTCCGAAGTCCTGCTGCGGTGCTCCACCTCTCCAGCCGCAGAACCACCTCAC
















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|86505454|gb|CI148087.1|CI148087
EST:     GAGACTTATGATACTCACAGTGATGCTTTTGAAATTGCACCTGCCTGCTG                         GATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTC
genomic: GAGACTTATGATACTCACAGTGATGCTTTTGAAATTGCACCTGCCTGCTGgtgtgtatct ... gctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTC
EST: gi|12622963|gb|AU173176.1|AU173176
EST:     GAGACTTATGATACTCACAGTGATGCTTTTGAAATTGCACCTGCCTGCTG                         GATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTC
genomic: GAGACTTATGATACTCACAGTGATGCTTTTGAAATTGCACCTGCCTGCTGgtgtgtatct ... gctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacttaattgatgatcctatatgctctatcgatatcttgttctgctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTCTGAGGTCTTGTTGCAGTGCTCCACCTCTCCAGCTGCCGAGCCACCACAT
       aattgat  putative branch site (score: 4)
                                         ttctgctc  putative PPT
     ttaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actattacaattcaaaatactagcacatgcatacttttctgggtaatcacttaattgatgatcctatatgctctatcgatatcttgttctgctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTCTGAGGTCTTGTTGCAGTGCTCCACCTCTCCAGCTGCCGAGCCACCACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - caaaatac
- - - - - - - - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctc