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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCATGGCGGGCAACAGAGGAGGCGATGCCGGGGAAGGGGAGTGGCTCAAGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacgagatgcatctcatccaattccaaccaaaacttactccatccgcaactgcatgaacgaattgaatttactcattctttcgttctttcttcc...

Basic information

species Oryza sativa
transcript LOC_Os01g70210.1
intron # 1
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|88454164|gb|CI694109.1|CI694109
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|568726|gb|D39575.1|D39575
EST:     AGGTCGCCGAGCTCAGGGCCACGGTNGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAA
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAA
EST: gi|33666128|gb|CF297095.1|CF297095
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGGAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|87012074|gb|CI291529.1|CI291529
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|88732258|gb|CI757106.1|CI757106
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|88441315|gb|CI602086.1|CI602086
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|86830184|gb|CI290357.1|CI290357
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|33662283|gb|CF293250.1|CF293250
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|33663142|gb|CF294109.1|CF294109
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|33664826|gb|CF295793.1|CF295793
EST:     AGGTCGCCGAGCTCATGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAA
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAA
EST: gi|58592472|gb|CF990780.1|CF990780
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|1631918|gb|C19647.1|C19647
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|88330797|gb|CI636807.1|CI636807
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|86830771|gb|CI293761.1|CI293761
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|55438121|gb|CV732354.1|CV732354
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCTTTACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|33665933|gb|CF296900.1|CF296900
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|33664298|gb|CF295265.1|CF295265
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|55439749|gb|CV733184.1|CV733184
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|88357222|gb|CI616109.1|CI616109
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|33677265|gb|CF305504.1|CF305504
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGCTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|88332251|gb|CI639278.1|CI639278
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC
EST: gi|88412243|gb|CI573519.1|CI573519
EST:     AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAG                         GAAGTGGACAACCTGACGCTGATGAGGTTCCTGCGGGCGCGAGACCACAAC
genomic: AGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAAC

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), 63 (downstream exon)
Score: 18

TGCCATGGCGGGCAACAGAGGAGGCGATGCCGGGGAAGGGGAGTGGCTCAAGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacg ... gcgcatgcagGAAGTGGACAACCTGACGCTGAGGAGGTTCCTGCGGGCGCGAGACCACAACGTGGAGAAGGCGTCGGCGATGCTGCTCAAGGCGCTCCGGTGGAGGAGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCATGGCGGGCAACAGAGGAGGCGATGCCGGGGAAGGGGAGTGGCTCAAGGTCGCCGAGCTCAGGGCCACGGTGGAAGCCCAGGACCCCCATGCCAAGgtacgcgacgagatgcatctcatccaattccaaccaaaacttactccatccgcaactgcatgaacgaattgaatttactcattctttcgttctttcttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccatcc