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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctcacttttttaccactccataccatatgctctaggcctgcttttatttcagagaagataaattaccatgagctaactgaaatcatcgtttacacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGGAACAAGTGGATCCCTTGATGGGCAACAAAGATTGGTTATAAAAGGAAGA

Basic information

species Oryza sativa
transcript LOC_Os03g21550.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 6
gtatgatctcacttttttaccactccataccatatgctctaggcctgcttttatttcagagaagataaattaccatgagctaactgaaatcatcgtttacacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGGAACAAGTGGATCCCTTGATGGGCAACAAAGATTGGTTATAAAAGGAAGA
||||||||  | ||  ||     |    ||||| ||   |            |||||| | |  |||||   |||      | || |||  ||| ||  |  ||| ||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||||||||| |||||||||||||| |||||||| |||||||||
gtatgatcctatttcgtt--tgatgatcaccatgtgtgttg-----------atttca-aaagaataaacagcca------agctaaaaggatcattctc-tttctagAATGCATAGGCAACCAGAACATGTGATGATGTTCTTGCTTGCTGAGATGGGAACAAGTGGATCCCTGGATGGGCAACAAAGGTTGGTTATCAAAGGAAGA
















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|88214500|gb|CI214349.1|CI214349
EST:     TTTGTG-ACTTCATGGATTTGTGCAAAAC                         AATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: TTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
EST: gi|9865576|gb|AU101326.1|AU101326
EST:     GAAGGCACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAAC                         AATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: GAAGGCACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
EST: gi|88205220|gb|CI205069.1|CI205069
EST:     ACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAAC                         AATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: ACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
EST: gi|58588566|gb|CF986874.1|CF986874
EST:     AAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAAC                         AATGC-GAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: AAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
EST: gi|58597410|gb|CK007938.1|CK007938
EST:     GAAGGCACAAAGAAGACAGTGTTTGTGAACTTCATGGATTTGTGCAAAAC                         AATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: GAAGGCACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
EST: gi|38478625|gb|CF962758.1|CF962758
EST:     GAAGGCACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGGGCAAAAC                         AATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: GAAGGCACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
EST: gi|89169705|gb|CI110064.1|CI110064
EST:     ACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAAC                         AATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG
genomic: ACAAAGAAGACAGTTTTTGTGAACTTCATGGATTTGTGCAAAACgtatgatctc ... acacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagagaagataaattaccatgagctaactgaaatcatcgtttacacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGGAACAAGTGGATCCCTTGATGGGCAACAAAGATTGGTTATAAAAGGAAGA
                        agctaac  putative branch site (score: 2)
                                              cacttcc  putative PPT
        aagataaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatctcacttttttaccactccataccatatgctctaggcctgcttttatttcagagaagataaattaccatgagctaactgaaatcatcgtttacacttccagAATGCATAGGCAACCTGAACATGTGATGATGTTTTTACTTGCTGAGATGGGAACAAGTGGATCCCTTGATGGGCAACAAAGATTGGTTATAAAAGGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA