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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgccccagcctcatagtaaaatatatttttattatttgatcttttcattgttttcataatagacataatataagggctaatgaaactgaatcttccttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 9
splice site 3'
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|58668338|gb|CK057024.1|CK057024
EST:     AATTGATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCAC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCAC
EST: gi|58656234|gb|CK044914.1|CK044914
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|33676232|gb|CF304471.1|CF304471
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|29642462|gb|CB647469.1|CB647469
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|218495881|gb|FG947063.1|FG947063
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|58608599|gb|CK036632.1|CK036632
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|29645565|gb|CB650572.1|CB650572
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|86848740|gb|CI294021.1|CI294021
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|33676868|gb|CF305107.1|CF305107
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|14192240|gb|AU184451.1|AU184451
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|33793137|gb|CF322449.1|CF322449
EST:     ATTTATGAGTGCCGTTAAGCAAATCTATGGTNGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: ATTTATGAGTGCCGTTAAGCAAATCTATGGT-GAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|58670000|gb|CK058686.1|CK058686
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|58681408|gb|CK070095.1|CK070095
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|29668942|gb|CB665217.1|CB665217
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCA-TCACA-CGCATTTGATTTGCT
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCT
EST: gi|58671508|gb|CK060194.1|CK060194
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|58665642|gb|CK054328.1|CK054328
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|33676662|gb|CF304901.1|CF304901
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
EST: gi|58597534|gb|CK008062.1|CK008062
EST:     AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAG                         TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC
genomic: AATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGC

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: 48 (upstream exon), 75 (downstream exon)
Score: 91

GAGTACCATGAGCTCATGGAAGAATTTATGAGTGCCGTTAAGCAAATCTATGGTGAGAAAGTTCTGATACAGgtctgcccca ... cttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcataatagacataatataagggctaatgaaactgaatcttccttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG
                        ggctaat  putative branch site (score: 91)
                                        tcttccttgt  putative PPT
     ataatagacataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgccccagcctcatagtaaaatatatttttattatttgatcttttcattgttttcataatagacataatataagggctaatgaaactgaatcttccttgtgccagTTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA