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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttattatagaattgtgcttgtatgttccgtagtgatgatatgtatgatggttaccagaaaggctaatgaattattgaccttatgatgtag

Basic information

species Oryza sativa
transcript LOC_Os10g11140.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G025854_T02 (Zea mays), 5'ss of exon 18
GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttattatagaattgtgcttgtatgttccgtagtgatgatatgtatgatggttaccagaaaggctaatgaattattgaccttatgatgtag
| |||||||||  | ||||||||  |||||||||| || ||||||||||| || ||||| |||||||||||||||||||| |||| |||   || | ||  |  || | |  |   |  ||||  ||  |   | ||  ||| |       |      | | ||  || ||||| ||
GCGTGTGAATCACACAGTGCAAACCAGATGATGGATCACCTTAGAGATGTTATGGCAAATAGCAAGCCTGGAGAGAAATACGgtttgtttgcat-gcatcctttttatctagttgctcttgattttactttgtaaggaaacctgctgaaaaatgatgctttcgattttgtgatgcag
















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|89198777|gb|CI003514.1|CI003514
EST:     GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|24468665|gb|CA305614.1|CA305614
EST:     ATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: ATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|24468739|gb|CA305688.1|CA305688
EST:     GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|88849912|gb|CI001618.1|CI001618
EST:     GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|86892654|gb|CI312043.1|CI312043
EST:     GAGCATCTTAGAGATGTGATCGCAAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GAGCATCTTAGAGATGTGATCGC-AAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|58611262|gb|CK038974.1|CK038974
EST:     GGAGCATCTTAGAGATGTGATCGCAAAGAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|44665085|gb|CR278519.1|CR278519
EST:     GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|86503671|gb|CI146304.1|CI146304
EST:     GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
EST: gi|29681951|gb|CB678226.1|CB678226
EST:     GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG                         GAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG
genomic: GGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttatt ... tatgatgtagGAAACTATACCCTTCAGTTTGCCGATGATTTCAGTTACACTGATCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATGgttggttattatagaattgtgcttgtatgttccgtagtgatgatatgtatgatggttaccagaaaggctaatgaattattgaccttatgatgtag

- - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA