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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGCTTCTGTTTCTACTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggctattattatttatgattcactagattgtcttttccctaaccacatggtcagtctagctgataatgtactgtttcttgtttgactgtcaaatg...

Basic information

species Oryza sativa
transcript LOC_Os03g44900.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G340749_T01 (Zea mays), 5'ss of exon 6
GGTGTTGCTTCTGTTTCTACTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggctattattatttatgattcactagattgtcttttccctaaccacatggtcagtcta-gctgataatgtactgtttcttgtttgactgtcaa-atg--
||||||||||||||| | ||||||||||||| |||||| ||||||||  | |||||||||| |||||||||    ||| | |||||||||  ||   | | ||||   || |  |   |  || | | |  | ||      ||     |||  | |   | ||| |  ||   
GGTGTTGCTTCTGTTCCGACTACTGCAGTTTCGAGTACAAAGAGTTCGATTGCAACTTCACTTACTCAGgttcatgctgtcattatttat--tttgatggtttgtggatttctca--tatttgataaataaatgccatctttgcttcttttaatatcaaagtgttagtattcc

upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AC197122.3_FGT003 (Zea mays), 5'ss of exon 9
GGTGTTGCTTCTGTTTCTACTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggctattattatttatgattcactagattgtcttttccctaaccacatggtcagtctagctgataatgtactgtttcttgtttgactgt-caaatg----
||||||||| ||||||| ||||||||||||||||| || ||||||||||| ||||||||||||||||||||    ||| |||||||||||  ||   | | ||||   | | ||||  |  || | | |  |  | |   | | ||  |     |||||   | | | |     
GGTGTTGCTCCTGTTTCGACTACTGCAGTTTTGAGCACAAAGAGTTCTGTTGCAACTTCACCTACTCAGgttcatgctgttattatttat--tttgatggtttgtgaat-ctctaat-atttgataaataaatgtca-gctttgcttctgtaaatttgaaattgctagtattcc
















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|58673547|gb|CK062233.1|CK062233
EST:     CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
EST: gi|58674781|gb|CK063468.1|CK063468
EST:     CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
EST: gi|58667792|gb|CK056478.1|CK056478
EST:     CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
EST: gi|58604983|gb|CK033016.1|CK033016
EST:     GAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: GAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
EST: gi|29630458|gb|CB635467.1|CB635467
EST:     CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
EST: gi|218484250|gb|FG949587.1|FG949587
EST:     CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
EST: gi|29638285|gb|CB643294.1|CB643294
EST:     CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAG                         GCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG
genomic: CTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggcta ... ttctctccagGCTACTGTATCAGCAGCTCCTTCGCTAAGTGTATCACAAGATCAAGCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGCTTCTGTTTCTACTACTGCAGTTTTGAGTACGAAGAGTTCTGTAGCAACTTCACCTACTCAGgtattggctattattatttatgattcactagattgtcttttccctaaccacatggtcagtctagctgataatgtactgtttcttgtttgactgtcaaatg

- - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - -  CGAAGA