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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGAGAGAGAAAATACAGCAGCAAGATGCTCTGCCGAAGCATGCTAACCCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagataaatctctcttgacgccacttgctgttcctgtatcctatgtttaagcatacttctaacgcccattctttttacag

Basic information

species Oryza sativa
transcript LOC_Os01g08560.1
intron # 9
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|86597100|gb|CI272695.1|CI272695
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTCCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86827202|gb|CI270888.1|CI270888
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86436862|gb|CI118584.1|CI118584
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|27921378|gb|CB097186.1|CB097186
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86517931|gb|CI158137.1|CI158137
EST:     CGTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|88831180|gb|CI081990.1|CI081990
EST:     GAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: GAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|58683636|gb|CK072323.1|CK072323
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86477603|gb|CI120236.1|CI120236
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86482608|gb|CI125241.1|CI125241
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|87022775|gb|CI269711.1|CI269711
EST:     CCTGTCCTACTCTCTCCTGATTTAAAGAAAAAGGCCGAAACGGCTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|29678339|gb|CB674614.1|CB674614
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86481493|gb|CI124126.1|CI124126
EST:     TACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGA
genomic: TACTCTCTTCTGATTTAAAGAAAAAGGCCGAAAC-GGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGA
EST: gi|86478387|gb|CI121020.1|CI121020
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|29680266|gb|CB676541.1|CB676541
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|87027774|gb|CI274338.1|CI274338
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|218478821|gb|FG953668.1|FG953668
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|87021150|gb|CI271957.1|CI271957
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|29619081|gb|CB624093.1|CB624093
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|87023343|gb|CI272171.1|CI272171
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|89184593|gb|CI007018.1|CI007018
EST:     AAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: AAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86876364|gb|CI318383.1|CI318383
EST:     CTACTCTCTTGTGATTTAAAGAAAAAGGCCGAAAC-GTTGACA-                         GTTCTGCAAACCGATAATTATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|88197475|gb|CI196782.1|CI196782
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86479448|gb|CI122081.1|CI122081
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|87018611|gb|CI254319.1|CI254319
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|89195759|gb|CI007178.1|CI007178
EST:     ATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: ATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|27553959|gb|CA997859.1|CA997859
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|58588974|gb|CF987282.1|CF987282
EST:     CCTGTCCTACTCTCGTGTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86422734|gb|CI060307.1|CI060307
EST:     AAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: AAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|218497201|gb|FG952163.1|FG952163
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86478003|gb|CI120636.1|CI120636
EST:     AAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: AAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|88906498|gb|CI375570.1|CI375570
EST:     TCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: TCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|87016407|gb|CI273617.1|CI273617
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|58600907|gb|CK011435.1|CK011435
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|88578902|gb|CI687862.1|CI687862
EST:     CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
EST: gi|86521850|gb|CI162056.1|CI162056
EST:     CTGATTTAAAGAAAAAGGCCGAAACGGTTGACAG                         GTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC
genomic: CTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGAC

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), 61 (downstream exon)
Score: 47

GGCTGAGAGAGAAAATACAGCAGCAAGATGCTCTGCCGAAGCATGCTAACCCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagat ... ctttttacagGTTCTGCAAACCGATAATGATGAAGCCGAAACCAGCTCCTAAGCCACAGACGCCCCCACAAACGCCACCGACCGAGACCCCGGCTGGCGGAGCCCAAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGAGAGAGAAAATACAGCAGCAAGATGCTCTGCCGAAGCATGCTAACCCTGTCCTACTCTCTTCTGATTTAAAGAAAAAGGCCGAAACGGTTGACAGgtccgtagataaatctctcttgacgccacttgctgttcctgtatcctatgtttaagcatacttctaacgcccattctttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA