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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTCTACATGGGCGGCGCCGATCGGACCGGCCGCCCCATCCTCCTCGCCTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctccgttggattcatattctcctaccataatgacactaccattacaatcactgacgtgtgggggaatagaaggttggaacccatataccggtaa...

Basic information

species Oryza sativa
transcript LOC_Os01g70210.1
intron # 2
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|33666128|gb|CF297095.1|CF297095
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|33662283|gb|CF293250.1|CF293250
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|33663142|gb|CF294109.1|CF294109
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|58592472|gb|CF990780.1|CF990780
EST:     CTTCCCCGGCAAGCACTTCTCCGCCAAACGCGAGATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGGATCCC
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGGATCCC
EST: gi|1631918|gb|C19647.1|C19647
EST:     TTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTTTNCAAG
genomic: TTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTT-CAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|55438121|gb|CV732354.1|CV732354
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|33665933|gb|CF296900.1|CF296900
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGGATC
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGGATC
EST: gi|33664298|gb|CF295265.1|CF295265
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|27577459|gb|CB000154.1|CB000154
EST:     CTTNNNNNNNTAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|55439749|gb|CV733184.1|CV733184
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|33677265|gb|CF305504.1|CF305504
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|33662282|gb|CF293249.1|CF293249
EST:     TAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: TAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|11565074|gb|AU165710.1|AU165710
EST:     CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: CTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
EST: gi|18385341|gb|BM418540.1|BM418540
EST:     TGCCTAAGTTCAAGA                         GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG
genomic: TGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG

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: 75 (upstream exon), 39 (downstream exon)
Score: 41

AAGGTCTACATGGGCGGCGCCGATCGGACCGGCCGCCCCATCCTCCTCGCCTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctcc ... tgcaccgcagGTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGTCTACATGGGCGGCGCCGATCGGACCGGCCGCCCCATCCTCCTCGCCTTCCCCGCCAAGCACTTCTCCGCCAAACGCGACATGCCTAAGTTCAAGAgtacgtctccgttggattcatattctcctaccataatgacactaccattacaatcactgacgtgtgggggaatagaaggttggaacccatataccggtaa

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