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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaaaaaataatatcagtgtcactcctgagttatgaacatggcaataaattgcgtactaatgttttcttatcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAGCTGTTCACCTCAAGATAACAGTTCAGAGGCTCTGAAAACAGACTCCAAC

Basic information

species Oryza sativa
transcript LOC_Os03g17570.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17570.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G095727_T03 (Zea mays), 3'ss of exon 9
gtgcaaaaaataatatcagtgtcactcctgagttatgaacatggcaataaattgcgtactaatgttttcttatct-tgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAGCTGTTCACCTCAAGATAACAGTTCAGAGGCTCTGAAAACAGACTCCAAC
|||||||| ||||||||||||||| | ||  ||||| |||||  || ||| |||| | ||||    || | || | |||||||||||||||| |||||||||| ||||||||||||||  ||| ||||| ||||| |||||| |||||||||||||| |||||  ||||||| ||||| |  
gtgcaaaacataatatcagtgtcattactaggttattaacataacagtaagttgcatgctaacccattatgatttctgcaagGTACCATACATCTGTGGCTTCCAATCAAGGTGGAGCAAGATATGGGGAAAGCTCTTCACCACAAGATAACAGTTCTGAGGCCATGAAAACGGACTCTACA
















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|29641996|gb|CB647003.1|CB647003
EST:     TGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAG                         GTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
genomic: TGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAGgtgcaaaaaa ... atcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
EST: gi|29642367|gb|CB647374.1|CB647374
EST:     CATGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAG                         GTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
genomic: CATGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAGgtgcaaaaaa ... atcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
EST: gi|428143|gb|D24291.1|D24291
EST:     CAGATCTCTCAGCTTTCACCAG                         GTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
genomic: CAGATCTCTCAGCTTTCACCAGgtgcaaaaaa ... atcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
EST: gi|58682152|gb|CK070839.1|CK070839
EST:     CAGCTTTCACCAG                         GTACCA-A-AACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
genomic: CAGCTTTCACCAGgtgcaaaaaa ... atcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
EST: gi|58688913|gb|CK077600.1|CK077600
EST:     CATGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAG                         GTACCATACAACTGTGGCTTCTAATCA
genomic: CATGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAGgtgcaaaaaa ... atcttgcaagGTACCATACAACTGTGGCTTCTAATCA
EST: gi|88960958|gb|CI382639.1|CI382639
EST:     CATGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAG                         GTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG
genomic: CATGATGAACGAAATATTCTGAAAAGATCAGATCTCTCAGCTTTCACCAGgtgcaaaaaa ... atcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgagttatgaacatggcaataaattgcgtactaatgttttcttatcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAGCTGTTCACCTCAAGATAACAGTTCAGAGGCTCTGAAAACAGACTCCAAC
                              tactaat  putative branch site (score: 1)
                                    tgttttcttatctt  CT-rich tract
                                 taatgttttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaaaaaataatatcagtgtcactcctgagttatgaacatggcaataaattgcgtactaatgttttcttatcttgcaagGTACCATACAACTGTGGCTTCTAATCAAGGTGGAGCTGGATTTGGGGGAAGCTGTTCACCTCAAGATAACAGTTCAGAGGCTCTGAAAACAGACTCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT