Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataatccagatcatattttcctttgcagcatttgaaatatttcatcttagcttattaatctatctactattggttctaagattctgtatgaattgttatttcatgatattttggcgaactgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTTCTTGAGCATTGCCGGGAAGACATGGAATTCATGGTGAAAAATTACGATA

Basic information

species Oryza sativa
transcript LOC_Os01g27520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27520.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G083836_T01 (Zea mays), 3'ss of exon 2
gtaaataatccagatcatattttcctttg-cagcatttgaaatatttcatcttagcttattaatctatctactattggttctaagattctgtatgaattgttatttca-tgatattttggcgaactgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTTCTTGAGCATTGCCGGGAAGACATGGAATTCATGGTGAAAAATTACGATA
|||| ||| |   |||  ||||  |||     ||| ||||| |  ||   ||  |   |  |   ||||       |  | | | | |  |||  ||  ||  ||  | ||||| | ||   ||||||  | |||||||| |||||||||||||||| ||||||||||||||||||||||||||| ||||| ||||||| |||||| ||||| || |||||||||||||| ||||
gtaactaagctgaatcgaatttgtcttcaattgcagttgaattgattttcctcggtacaaaa---tatcc------gactatgaaagttagtaaaaacagtctttgaagtgatagtatgtttaactgttctgcagGATGACATGAACTGTGCAGAAAAATATGTACAGTACCTTTGCAAGTGGCTGCTTGACCATTGCCAGGAAGATATGGAGTTTATGGTGAAAAATTATGATA
















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|163920588|gb|EG709595.1|EG709595
EST:     TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
EST: gi|163927289|gb|EG715208.1|EG715208
EST:     TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
EST: gi|163926765|gb|EG715053.1|EG715053
EST:     TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
EST: gi|58679918|gb|CK068605.1|CK068605
EST:     TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
EST: gi|58589280|gb|CF987588.1|CF987588
EST:     TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
EST: gi|66917235|gb|CX104083.1|CX104083
EST:     TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
EST: gi|29614514|gb|CB619527.1|CB619527
EST:     TGGCAGAGTTTTGGATGGTTGANCCAGAAATCGCATTTGCTAACTTGCAG                         GATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT
genomic: TGGCAGAGTTTTGGATGGTTGAACCAGAAATCGCATTTGCTAACTTGCAGgtaaataatc ... tgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaagattctgtatgaattgttatttcatgatattttggcgaactgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTTCTTGAGCATTGCCGGGAAGACATGGAATTCATGGTGAAAAATTACGATA
                aattgttatttcatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataatccagatcatattttcctttgcagcatttgaaatatttcatcttagcttattaatctatctactattggttctaagattctgtatgaattgttatttcatgatattttggcgaactgtgttccagGATGATATGAACTGTGCAGAAAGATATGTACAGTACCTTTGCAAGTGGCTTCTTGAGCATTGCCGGGAAGACATGGAATTCATGGTGAAAAATTACGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA