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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcaccgcatcttaaatctgttgtgtttattcttttatatgcaatcagcttagatagttgcctgaataattctttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 10
GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcaccgcatcttaaatctgttgtg-tttattcttttatatgcaatcagcttagatagttgcctgaataattctttgcag
||||||||||||||||| ||||||||||| || ||||| |||||||||||| ||| |   ||   || || ||||  |||  | |||| | | |||||| || |  || |||| || ||||||| ||||||
GCATTGGAGCGAATGGAACATGTTGATGCAGTTGTCAGCGATCCAGAgtatgtcatc---tccctaaactattgtactttggtattttgtttacaatcaactcat-taattgcttggataattccttgcag

upper sequence: LOC_Os02g58020.3 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S47_97V6.2 (Physcomitrella patens), 5'ss of exon 10
GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcaccgcatcttaaatctgttgtgtttattcttttatatgcaatcagcttagatagttgcctgaataattctttgcag---------------------
|| ||||||||||| |  ||||||||||| ||||||| |||||||||||   |   |  || || ||  || | ||||       |   |||||| ||  |||    |  |     || |   ||| ||                      
GCTTTGGAGCGAATCGGCCATGTTGATGCAGTCGTCAATGATCCAGAgtgagtatgcatatttttaa--tgct-tgttctactggtcgcatgcaa-cattttatgacggagtacagatgaggttttacatcaggatgtaactaatttaaaa
















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:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|29662747|gb|CB659022.1|CB659022
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|3766930|gb|AU031040.1|AU031040
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|29676044|gb|CB672319.1|CB672319
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|27546087|gb|CA764161.2|CA764161
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|24468674|gb|CA305623.1|CA305623
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|218495876|gb|FG947058.1|FG947058
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|29662748|gb|CB659023.1|CB659023
EST:     TGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTAT-AATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: TGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|218483226|gb|FG956166.1|FG956166
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
EST: gi|86909957|gb|CI292894.1|CI292894
EST:     GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGA                         CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT
genomic: GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcacc ... ttctttgcagCTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTGGAGCGAATGGAGCATGTTGATGCGGTCGTCAGTGATCCAGAgtatatcaccgcatcttaaatctgttgtgtttattcttttatatgcaatcagcttagatagttgcctgaataattctttgcag

-  TTGGAG
- - - - - - - GGAGCA