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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattactgcttttttttctcttttcttttccatataatttgcaatctgcagttgctgttcgatcttcatgccagagtactttgttgattgcaaatt...

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 4
splice site 5'
intron type U2

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|88344389|gb|CI677431.1|CI677431
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88721114|gb|CI744413.1|CI744413
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTG
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTG
EST: gi|58591551|gb|CF989859.1|CF989859
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|58670757|gb|CK059443.1|CK059443
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|33653794|gb|CF276408.1|CF276408
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88354143|gb|CI637709.1|CI637709
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAA
EST: gi|58672555|gb|CK061241.1|CK061241
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|38568445|gb|CD670660.1|CD670660
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88717903|gb|CI739415.1|CI739415
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGA
EST: gi|58689760|gb|CK078447.1|CK078447
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88722467|gb|CI745977.1|CI745977
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTG
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTG
EST: gi|88408710|gb|CI686220.1|CI686220
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88363053|gb|CI616210.1|CI616210
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGG
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGG
EST: gi|58665042|gb|CK053728.1|CK053728
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|58594766|gb|CF993074.1|CF993074
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88575546|gb|CI669691.1|CI669691
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88408685|gb|CI686192.1|CI686192
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATNTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|58599157|gb|CK009685.1|CK009685
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88330972|gb|CI638380.1|CI638380
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88586453|gb|CI704154.1|CI704154
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGACCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|29636698|gb|CB641707.1|CB641707
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|58591384|gb|CF989692.1|CF989692
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|117233824|gb|CT847763.1|CT847763
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|58586261|gb|CF984569.1|CF984569
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88353573|gb|CI632964.1|CI632964
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|25797720|gb|CA753681.1|CA753681
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|66912833|gb|CX099681.1|CX099681
EST:     CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|12404688|gb|AU166289.1|AU166289
EST:     ATTCCGAGAAAG                         GTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
genomic: ATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCA
EST: gi|88744711|gb|CI768071.1|CI768071
EST:     CGTCGGGAGCGGNGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG                         GTATCGAGCTGATCCTG
genomic: CGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTG

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: 61 (upstream exon), 73 (downstream exon)
Score: 49

ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattac ... aatgttgcagGTATCGAGCTGATCCTGAGCACCGAAATTGTCAAGGCTGATCTTGCCTCCAAGACATTGACCAGTTCAGCTGATGCAACCTTTACCTATGACACTTTGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAGgtacaattactgcttttttttctcttttcttttccatataatttgcaatctgcagttgctgttcgatcttcatgccagagtactttgttgattgcaaatt

- - - - - - - - - - - - - - - - - - - - - - -  GAGAGG