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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtctcaactctcaactcacgacattgccagttaccatcgctttaccgcaaaatatttacattataatttacacagaaaagtttcaattgattcctgattccaccttcatcttacttgcgcag

Basic information

species Oryza sativa
transcript LOC_Os03g57130.1
intron # 8
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|15854078|gb|BI806874.1|BI806874
EST:     CTGCCTCCCCAACGCGCTGTAAGATGGAACCCTC-ACAACTTCCTCCAG                         GATGATCATGTCACAAGGCAGTTGGCTCCAGCAGCTGCTGCACAACATGAC
genomic: CTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGC-GTTGGCTCCAGCAGCTGCTGCACAACATGAC
EST: gi|87026215|gb|CI252365.1|CI252365
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|87010056|gb|CI279153.1|CI279153
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88485325|gb|CI422596.1|CI422596
EST:     GCTGCCTCCCCAACGCGGTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|89198053|gb|CI117531.1|CI117531
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|89198745|gb|CI003482.1|CI003482
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|12622771|gb|AU172984.1|AU172984
EST:     CCTCAACAACTTCCTCCAG                         GATGATCATGTCNCAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: CCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|86504776|gb|CI147409.1|CI147409
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|87029166|gb|CI276434.1|CI276434
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88514299|gb|CI441805.1|CI441805
EST:     CAACAACTTCCTGCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: CAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|86504154|gb|CI146787.1|CI146787
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88519245|gb|CI446899.1|CI446899
EST:     ATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: ATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88227912|gb|CI227392.1|CI227392
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88272723|gb|CI386578.1|CI386578
EST:     CCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: CCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88239243|gb|CI240405.1|CI240405
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|86494403|gb|CI137036.1|CI137036
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|87011439|gb|CI279348.1|CI279348
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|88205866|gb|CI205715.1|CI205715
EST:     CCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: CCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|86501806|gb|CI144439.1|CI144439
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
EST: gi|86598079|gb|CI278469.1|CI278469
EST:     GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG                         GATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT
genomic: GCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACT

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: 69 (upstream exon), 62 (downstream exon)
Score: 29

GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtct ... acttgcgcagGATGATCATGTCACAAGGCGTTGGCTCCAGCAGCTGCTGCACAACATGACTATGGCCGGCATGGGAGGAGCTCCTCATGGAGGCCTTGATCACATCATGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAGgtgtgtgtctcaactctcaactcacgacattgccagttaccatcgctttaccgcaaaatatttacattataatttacacagaaaagtttcaattgattcctgattccaccttcatcttacttgcgcag

- - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - -  GATGGA