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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcatgcagcacttttactcaattccgtgagcataactagccccgctgctcaccttccactttgttttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g41880.1
intron # 4
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|88957420|gb|CI095361.1|CI095361
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|88833647|gb|CI077128.1|CI077128
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|89173605|gb|CI041498.1|CI041498
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACCAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|88980779|gb|CI022473.1|CI022473
EST:     CTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACCAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: CTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|86259869|gb|CI065742.1|CI065742
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|87010723|gb|CI312415.1|CI312415
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|66913309|gb|CX100157.1|CX100157
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|86502604|gb|CI145237.1|CI145237
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|88833514|gb|CI076995.1|CI076995
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTTATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|286956|gb|D15763.1|D15763
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
EST: gi|25799923|gb|CA755884.1|CA755884
EST:     TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTG                         GGTTTTGACAAGGNCAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC
genomic: TGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACC

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: 71 (upstream exon), 67 (downstream exon)
Score: 33

ACTGAAGGTTGAAGAGAGAAAGGTTGTGGTGGACAAGGAATTGCAGTCAATGCAACAGCTCTCAGTGAAGAAGGATTCTGATGAAGTGTTCATCAAGCTGgtaggttcat ... tttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattccgtgagcataactagccccgctgctcaccttccactttgttttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG
                                ccttccactttgtttt  CT-rich tract
                                        tttgttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcatgcagcacttttactcaattccgtgagcataactagccccgctgctcaccttccactttgttttaatgcagGGTTCTGACAAGGACAAAAAGAAAGAAAATGTTGAAAGAGATGAACGCACCAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG