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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
gtatg----ttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatc-tgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG
|||||     | ||||| | |||||||  || |   |  | ||  ||     |  || |  | | | ||  | ||   |  |   ||   | ||  | || |||||||||||||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| || ||||||||||||
gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
----gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG
     |||    ||||   |     |   |  |   ||  ||| ||  |    ||  ||   | |||    || | | | |     | |||  ||  |  || |||||||||| || |||||||||||||| || |||||||||||  ||||  |||| ||||||||||| | ||| ||||| || ||||| ||| | |||
tactatataaacctttttgtgggggagaatgttgttaa--aataatgac----atgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 11
gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatac----atcttttttttggtctcatgtttgatctgtta----tttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG
           | ||  |   | ||   |     |||||| ||  ||  ||     || ||  |    || || ||| ||   | | | ||  |   | |    || |||||||||| |||||||||||||||||||| |||||||||||  ||||  |||| ||||||||||| | ||| ||||| || ||||| ||| | |||
---------agtactaaataaacctgtgtgggggagaatgttat-taaaataatgacatgactctggtatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCAAATGGTATTGGCAAATCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGATCTGCTAAG

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|427530|gb|D23597.1|D23597
EST:     AAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: AAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|27576082|gb|CA998776.1|CA998776
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|29623431|gb|CB628442.1|CB628442
EST:     TTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: TTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|3766930|gb|AU031040.1|AU031040
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|29676044|gb|CB672319.1|CB672319
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|27546087|gb|CA764161.2|CA764161
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|29676045|gb|CB672320.1|CB672320
EST:     AAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: AAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|218495876|gb|FG947058.1|FG947058
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|29664090|gb|CB660365.1|CB660365
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|29662748|gb|CB659023.1|CB659023
EST:     CTTATNTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|218483226|gb|FG956166.1|FG956166
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
EST: gi|29644367|gb|CB649374.1|CB649374
EST:     CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG
genomic: CTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAAgtatgttgct ... gttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG
                                    gtttgat  putative branch site (score: 5)
                                              ttatttc  putative PPT
             atacatctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatctgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC