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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagcttaattgggctatctgaaaacattcaactactatgtgcaattaaatccttattgaaaaatcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 8
aaaagcttaattgggctatctgaaaac-attcaac-tactatgtgcaattaaatccttattgaaaaatcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
 ||     | ||    || ||| ||||  |||||  || ||   ||   |  ||  ||  |  || |    || || |    ||  |  || |||||||||| |||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||
gaacagaaattttaaatacctggaaactgttcaagatattaatcgcttctcgatattttctcgaagac--gagggatgaactttcattgtttttctgtgtagACATTCATTGACAAGTTTCGGTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG

upper sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 7
aaaagcttaat-tgggctatctgaaaacattcaactactatgtgcaattaaatccttattgaaaa----atcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
||||| ||  | |  ||||| || | |     |  |  | ||   | |||     ||| | || |    || ||  |||  |||  || | |   ||      || | |||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||||
aaaagattgctgtttgctatttgcaga-----acttgttgtgcatatttagcattttaatcaagattctattgacatgacatttgatgttttgcttttctgccagACCTTCATTGACAAGTTCCGTTATAATGCGAAGAGGGCATCACTTGTTCAATCTAGAATCAAG

upper sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 7
aaaagcttaat-tgggctatctgaaaacattcaactactatgtgcaattaaatccttattgaaaaatcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
||||| ||  | |  || || || | |  ||   |  || |  ||| || ||||   |||  |      |  |||  |||  || | |   ||      || | |||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||||
aaaagattgctgtttgcaatttgcagaacttgtgcctctgta-gcattttaatcaagattctatttgacatatgacttttgatgttttgcttttctatcagACCTTCATTGACAAGTTCCGTTATAATGCGAAGAGGGCATCACTTGTTCAATCTAGAATCAAG

upper sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------aaaagcttaattgggctatctgaaaacattcaactactatgtgcaattaaatccttat-tgaaaaatcgaagtgaagtttattggtctttcttctg-tgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
                      |  | || |      || | |  ||    ||  ||  | |||  ||| | || |  |  ||  |  |     ||| | ||  |    | | ||||| |  |||| |||||||| || || ||||||||||||||||| || || |||||||| ||||||||||||
gtttcttttcttcttctggaaaatgaactcataaattctgtttccaactcgtct-ctggtttgtttaataatattccaacatgggatgtaagtttgatgcttgatatcttgttttctgctacagGCGTTCATTGATAAATTTCGTTACAATGCAAAGAGGGCGTCTCTTGTTCAGTCAAGAATCAAG

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|27576082|gb|CA998776.1|CA998776
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|29662747|gb|CB659022.1|CB659022
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|3766930|gb|AU031040.1|AU031040
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|29676044|gb|CB672319.1|CB672319
EST:     GAGAAGGCCAGATCCCATATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: GAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|27546087|gb|CA764161.2|CA764161
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|24468674|gb|CA305623.1|CA305623
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTTGTTCA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTT-GTTCA
EST: gi|218495876|gb|FG947058.1|FG947058
EST:     GGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: GGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|218483226|gb|FG956166.1|FG956166
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|86909957|gb|CI292894.1|CI292894
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
EST: gi|58602069|gb|CK012597.1|CK012597
EST:     ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAG                         GCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA
genomic: ACCAGCAGAAAGCTTTTGAAACAAATGAGAAGGCCAGATCCCACATGCAGgttggatctg ... ttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaatccttattgaaaaatcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG
                                   ttggtctttcttct  CT-rich tract
         ttattgaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagcttaattgggctatctgaaaacattcaactactatgtgcaattaaatccttattgaaaaatcgaagtgaagtttattggtctttcttctgtgtagGCATTCATTGACAAGTTCCGTTACAATGCAAAGAGAGCATCACTTGTTCAATCAAGAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA