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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATGAAGAATAACAATCCTGATTTGCCTACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattcagaacctctttctcatctaatatgtcccctgttgtatagcagagcactgttttcacgttttagcccccaactaattctttcatgttttctattgcattcttaaatactagtacatgacatgtgtgatgataatctcctttgcaccacgtcttgagcag

Basic information

species Oryza sativa
transcript LOC_Os01g08970.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08970.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G032252_T01 (Zea mays), 5'ss of exon 15
AATATGAAGAATAACAATCCTGATTTGCCTACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattcagaacctctttctcatctaatatgtcccctgttgtatagcagagcactgttttcacgttttagcccccaactaattctttcatgttttctattgcattcttaaatactagtacatgacatgtgtgatgataatctcctttgcaccacgtcttgagcag
|| ||||||| | ||| || ||||||||||| || ||||| ||||||||||| ||||||||||||||||||||| ||||||| |||| | | || |||||| ||| |||| ||| | ||||| | || | |||| | ||| ||| | ||| ||| | ||| | | | | |||| | | | | | | || | | |||||||
AACATGAAGAGCAGCAACCCAGATTTGCCTACGACTGAGATCGCAAAGAAGCTTGGGGAGATGTGGCAAAAGATGTCAGgtaagattccgga--tcgttctcagcta-tatga--------gta----atagcaccagtgctg----------ccaggcaaattttgcaatgctttgt----catgtttaca-gctaaaataaaagctttgtgcttacggt-ttttacgtcccttgccatgagcag

upper sequence: LOC_Os01g08970.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM5G877308_T01 (Zea mays), 5'ss of exon 2
AATATGAAGAATAACAATCCTGATTTGCCTACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattcagaacctctttctcatctaatatgtcccctgttgtatagcag-agcactgttttcacgttttagcccccaactaattctttcatgttttctattgcattcttaaatactagtacatgacatgtgtgatgataatctcctttgcaccacgtcttgagcag
|| ||||||| | ||| || ||||||||||| || ||||||||||||||||| ||||||||||||||||||||| || ||| ||||| | | | || | ||| | ||| |||| | ||| ||| | | |||||| | ||||||| ||| ||| | ||| |||| | | |||| | | | ||| || || ||| ||||||
AACATGAAGAGCAGCAACCCAGATTTGCCTACGACTGAGATTGCAAAGAAGCTTGGGGAGATGTGGCAAAAGATGTCAAgta-tattctagatcattctcc-----attatattatctgagtaatagtaccagcgctg----------------cgaggcaaattctgcaacgttttct----catgtttaca-gctaaaacataagctttgtgcttaccgtttccac-gctccttgtcacgagcag
















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|88725405|gb|CI748664.1|CI748664
EST:     GTGGTAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: GTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|86480966|gb|CI123599.1|CI123599
EST:     TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|27578065|gb|CB000760.1|CB000760
EST:     TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|88837167|gb|CI078527.1|CI078527
EST:     ACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: ACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|88955490|gb|CI091582.1|CI091582
EST:     CGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: CGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|29631305|gb|CB636314.1|CB636314
EST:     TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|86497001|gb|CI139634.1|CI139634
EST:     TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|218484541|gb|FG954362.1|FG954362
EST:     GAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: GAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|89189197|gb|CI048736.1|CI048736
EST:     TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCGACAGTCTCAAGTCGACAAGAAACGAT
genomic: TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|86480956|gb|CI123589.1|CI123589
EST:     TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: TACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT
EST: gi|88837509|gb|CI078869.1|CI078869
EST:     GGAGATGTGGCAAAAGATGACAG                         GCGAAGAGAAGCAACCTGACATCCAACAGTCTCAAGTCGACAAGAAACGAT
genomic: GGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 73 (downstream exon)
Score: 58

AATATGAAGAATAACAATCCTGATTTGCCTACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattca ... tcttgagcagGCGAAGAGAAGCAACCTTACATCCAACAGTCTCAAGTCGACAAGAAACGATACGAGAAGGAATCTGCTGTCTACCGTGGCGCAGCCGCCATGGACGTGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATGAAGAATAACAATCCTGATTTGCCTACAACCGAGATTGCAAAGAAGCTCGGGGAGATGTGGCAAAAGATGACAGgtaatattcagaacctctttctcatctaatatgtcccctgttgtatagcagagcactgttttcacgttttagcccccaactaattctttcatgttttctattgcattcttaaatactagtacatgacatgtgtgatgataatctcctttgcaccacgtcttgagcag

- - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG