Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctttgcctttctgtgagaagttctttaatttggtcatgtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT

Basic information

species Oryza sativa
transcript LOC_Os02g40890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G060870_T02 (Zea mays), 3'ss of exon 5
--ggctttgcctttctgtgagaagttctttaatttggtcat-gtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT
       | |  || |  ||  | | | |   ||||||    || |    | |||||| |   | | ||| |||||     |||| ||||||     ||||||||||| ||||||||  ||||||||||||| ||||| |||||||||||||||||||| ||||| || || || ||||| |||||||| ||||||||||| |
tcaatgctcctcttttaagatcattgcatacttttggttggagtatatcccttttattgg---tgcttccatttgttcatttgcttatatgaattgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G125556_T01 (Zea mays), 3'ss of exon 5
---ggctttgcctttctgtgagaagttctttaattt-ggtcatgtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT
        ||   || |  || |  ||   |  |||  ||||| | |   || ||||||||   ||  ||  |||||     | || |||||||  || | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||| |||||||| ||||||||||| |
ttcattcctgatcttttaagatagtttgcatgcttttagtcat-tatctctcttttatttgtgctt--tcattttgttgatttacttatatgagtgatcg-cagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
















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|88476057|gb|CI413328.1|CI413328
EST:     CAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88504138|gb|CI431644.1|CI431644
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|86600278|gb|CI356035.1|CI356035
EST:     CATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88262804|gb|CI364382.1|CI364382
EST:     AAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: AAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88848293|gb|CI086815.1|CI086815
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|9865530|gb|AU101280.1|AU101280
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|86432844|gb|CI086455.1|CI086455
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|86880405|gb|CI320946.1|CI320946
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGC-TGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTANT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|66914261|gb|CX101109.1|CX101109
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88277826|gb|CI398628.1|CI398628
EST:     GCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: GCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|33807484|gb|CF329619.1|CF329619
EST:     CAAAACTCTGAAGAAATGGCATGGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAAAAATT-ATGGAGGTCATTAGT
genomic: CAAAACTCTGAAGAAATGGCATGG-TTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|396941507|gb|HO188716.1|HO188716
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|87028768|gb|CI349487.1|CI349487
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|33657910|gb|CF280524.1|CF280524
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|396941616|gb|HO188273.1|HO188273
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|86414401|gb|CI068804.1|CI068804
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88280229|gb|CI401427.1|CI401427
EST:     TTGGCTTGCCAGTTCTAGTTTTACA                         CTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: TTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88507701|gb|CI435207.1|CI435207
EST:     GGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: GGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|33807485|gb|CF329620.1|CF329620
EST:     GAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAAAAATTTATGGAGGTCATTAGT
genomic: GAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|86882400|gb|CI325805.1|CI325805
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|157650062|gb|EX449696.1|EX449696
EST:     GTTGGCTTGCCAATTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: GTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|163918588|gb|EG711638.1|EG711638
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|58696097|gb|CK084784.1|CK084784
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATCAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88508201|gb|CI435707.1|CI435707
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88236949|gb|CI236798.1|CI236798
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|88491720|gb|CI428992.1|CI428992
EST:     CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACA                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAAACTCTGAAGAAATGGCATGGTTGGCTTGCCAGTTCTAGTTTTACAgttgagtcgt ... aaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT
     ttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctttgcctttctgtgagaagttctttaatttggtcatgtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT