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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaggttatggagcgttggtggtgttgttttttgtgggtggttcgaggtgaatcggtgggttgattcctgattttgctgtttgttttggctgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g03070.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G093050_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------gtaggttatggagcgttggtggtgttgttttttgtgggtgg---ttcgaggtgaatcggtgggttgattcctgattttgctgtttgttttggctgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG
                                                 | | |    |   ||| |       ||||||||          |  |  ||  ||   |  | |   |||     |  ||||| || | ||    |  ||||| ||||||||    |  |||     | || ||   |||||||| ||||||||||||||||||||||| |||||||| || |
gtattgccaaaatgagttcccaaactctaatctcaaactatttggctgtttgatcgatgcctgttagcttctaagttttttgcaaaaaaatatcgggtgtacatgcctttgctagatcccaccctaactgttggtgt-ggtgcagGAGAAGGAGTAGATCGTCGACCCAGA-----ACCCTCGCTGATGGCGACTTTCGCGAAACCTGAGAACGCGCTGAAGAGAGCCGAAG
















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|88370850|gb|CI592616.1|CI592616
EST:     CGGACGGCCGTACGGCGCCGTACACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88726955|gb|CI750610.1|CI750610
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88310182|gb|CI657606.1|CI657606
EST:     CGGACGGCCGTACGGGGCCGTCAACCGCGCACGTTTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88364312|gb|CI612261.1|CI612261
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88347801|gb|CI655154.1|CI655154
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88352152|gb|CI613803.1|CI613803
EST:     CGGACGGGCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGGGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88730926|gb|CI754539.1|CI754539
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88314718|gb|CI608177.1|CI608177
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88390540|gb|CI609165.1|CI609165
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88316752|gb|CI624194.1|CI624194
EST:     CGGACGGCCGTACGGCGCCGTCCAACGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGGCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88736241|gb|CI759749.1|CI759749
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88719635|gb|CI743145.1|CI743145
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88423421|gb|CI576546.1|CI576546
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTAGAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88312839|gb|CI589935.1|CI589935
EST:     CGGAGGGCCGTACGGCGCCGTCCACCGCGCACGTTTCCGGCGATATACAG                         GTGTAGATCGCTTCCGGAGACAT-CAACCGCGGCCATGGCGACCTTAGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|29626201|gb|CB631212.1|CB631212
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88421421|gb|CI569861.1|CI569861
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88403718|gb|CI611373.1|CI611373
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88731382|gb|CI754995.1|CI754995
EST:     CGGACGGCCGTANGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88314010|gb|CI600012.1|CI600012
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88352132|gb|CI613783.1|CI613783
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGTTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88316017|gb|CI618893.1|CI618893
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTAAAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88311895|gb|CI577501.1|CI577501
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88389001|gb|CI595235.1|CI595235
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATAGCTTCCGGAGAAATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
EST: gi|88367768|gb|CI570507.1|CI570507
EST:     CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAG                         GTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA
genomic: CGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGA

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: 49 (upstream exon), 71 (downstream exon)
Score: 78

ACCCCCCATTCCCATCCCCTCCACCCAGATCGCCGCCGCCGCCTTCGCCTCGGACGGCCGTACGGCGCCGTCCACCGCGCACGTCTCCGGCGATCTACAGgtatcgtcgc ... tgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtgaatcggtgggttgattcctgattttgctgtttgttttggctgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG
                    tcctgat  putative branch site (score: 78)
                                  tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttatggagcgttggtggtgttgttttttgtgggtggttcgaggtgaatcggtgggttgattcctgattttgctgtttgttttggctgtgatgaagGTGTAGATCGCTTCCGGAGACATCCAACCGCGGCCATGGCGACCTTCGCGAAACCTGAGAACGCGCTCAAGAGAGCGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - -ggtggtg
- - - - - - - - - - - - - - - - - - - - - - - -gtgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgctg