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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttatcatgccatattgtcttcatgtccaaacattaaggacaatactattgtgcaagatgttttctgcatctagcattttatcatcatacaatat...

Basic information

species Oryza sativa
transcript LOC_Os01g62900.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G028535_T02 (Zea mays), 5'ss of exon 19
GTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggtt----atcatgccatattgtcttc----atgtccaaacattaaggacaatactattgtg--caagatgttttctgcatctagcattttatcatcatacaatat-----------
||||||||||| |||| |||||||||||| || || |||||||| ||||||||||| ||||| ||||| |||||   ||    ||||    | | ||| |||     | |     | | | |||  || | | | |     | | | ||  | |    |     |  || | ||    |             
GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacatttttttatcacttgacaatgtgttccatggtatttgtccgtgagggaagatcccacttttactgacacgattattacgctcatgtcatactcgtgatctttttctccacatgtag
















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|88254967|gb|CI353791.1|CI353791
EST:     GGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: GGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|428854|gb|D25010.1|D25010
EST:     ATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: ATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|87028718|gb|CI349437.1|CI349437
EST:     CTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: CTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|44670561|gb|CR283995.1|CR283995
EST:     CGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: CGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|38471160|gb|CF955291.1|CF955291
EST:     ATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: ATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|88265249|gb|CI369023.1|CI369023
EST:     TCGGGGGCCTGTT-GCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: TCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|88273346|gb|CI388802.1|CI388802
EST:     GGCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
genomic: GGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA
EST: gi|88261597|gb|CI365173.1|CI365173
EST:     ATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG                         CATTTTACGAGGAAGTGGACAAGTAGTGAACGCCGACAAGGGAGTTGTTTA
genomic: ATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTA

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: 39 (upstream exon), 75 (downstream exon)
Score: 12

GTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttat ... ttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATGgtagggttatcatgccatattgtcttcatgtccaaacattaaggacaatactattgtgcaagatgttttctgcatctagcattttatcatcatacaatat

- - - - - - - - - - - - - - - - - - - - - - - - GATGGA