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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgattggttttttgttgtagtaatatagcaaacttgaaagaaaaacatgatgaggctagctgtatataaatcgaaactgaaagaggagcctctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGCAAGGAGATCGACTCGGACGATGATTCTCCACCAAGAAAACAGCAGGCAG

Basic information

species Oryza sativa
transcript LOC_Os07g01880.1
intron # 10
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|29636726|gb|CB641735.1|CB641735
EST:     ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
EST: gi|86597143|gb|CI272738.1|CI272738
EST:     ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
EST: gi|88845026|gb|CI083951.1|CI083951
EST:     ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
EST: gi|86840445|gb|CI342619.1|CI342619
EST:     ATGAGGAAGATGTGGAAGAAGAAGCACCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
EST: gi|29639167|gb|CB644176.1|CB644176
EST:     ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
EST: gi|86482587|gb|CI125220.1|CI125220
EST:     ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC
EST: gi|88991021|gb|CI108408.1|CI108408
EST:     ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAG                         GAACCAAAACGGAGGAGAGAATCTGGGGGTGACAGTGCCAGCCAAAGGCGC
genomic: ATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGC

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: 66 (upstream exon), 10 (downstream exon)
Score: 4

GCACTCACCAACCCAGGGGAGGGAAGATGAGCTTGATGAAGAAGATGAATATGAGGAAGATGTGGAAGAAGAAGCAGCCATGTCAGATGAAGAAATTGAGgtaagaccaa ... tctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGCAAGGAGATCGACTCGGACGATGATTCTCCACCAAGAAAACAGCAGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatgaggctagctgtatataaatcgaaactgaaagaggagcctctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGCAAGGAGATCGACTCGGACGATGATTCTCCACCAAGAAAACAGCAGGCAG
                                           cctctgct  CT-rich tract
                 tatataaatcgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgattggttttttgttgtagtaatatagcaaacttgaaagaaaaacatgatgaggctagctgtatataaatcgaaactgaaagaggagcctctgctgcagGAACCAAAACGGAGGAGAGAATCTGGGGGTGGCAGTGCCAGCCAAAGGCGCAAGGAGATCGACTCGGACGATGATTCTCCACCAAGAAAACAGCAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - -ttgttgt
- - - - - - - - - - - - - agcaaac
- - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - -catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagagga