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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttgtcccttatcttcatcatataatgtacagttctgtatagcgtaaaacattaccacctcatgtgttctctcatgttaattaaagcatcgatg...

Basic information

species Oryza sativa
transcript LOC_Os05g22970.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G125310_T01 (Zea mays), 5'ss of exon 3
ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttgtcccttatcttcatcatataatgtacagttctgtatagcgtaaaacattaccacctcatgtgttctctcatgttaattaaagcatcgatg
||||| ||||| ||||| ||||||||||| || ||||||||||| ||||||||||||||||||| |||||  |  |||    |      | |   || |    ||   ||   |||||| || || ||||| | |  |||        ||      |  |||
ATGTTACGTGTGAAGGACCCAAAAGTGAGCCTTGACTTCTACTCACGTGTGATGGGCATGTCgtgagtttaatttctttctcttcctccaaataatatatccatgctgagaaaaaaacaataacagctcatatctgttctttatagttttgtcctgtaaatg
















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|33818513|gb|CF335087.1|CF335087
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88343329|gb|CI627289.1|CI627289
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATT
EST: gi|33819107|gb|CF335378.1|CF335378
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88364009|gb|CI610353.1|CI610353
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTANTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTT-CCTGAGATGAAATTCAGCTTGTATTT-CT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88396511|gb|CI600994.1|CI600994
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|38478143|gb|CF962276.1|CF962276
EST:     GAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|66918847|gb|CX105695.1|CX105695
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|38482501|gb|CF966535.1|CF966535
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|87021271|gb|CI295330.1|CI295330
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCA
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCA
EST: gi|87034760|gb|CI189384.1|CI189384
EST:     TGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: TGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88329315|gb|CI653229.1|CI653229
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|25800681|gb|CA756642.1|CA756642
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|86599770|gb|CI255932.1|CI255932
EST:     AAGTGAAGTCTCGACTTCTACTCGCGTGTGATGGGCATTTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGTG-AGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|33813839|gb|CF332805.1|CF332805
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88364025|gb|CI610369.1|CI610369
EST:     AAGGATCCAAAAGTGAGTCTCGAATTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|58687672|gb|CK076359.1|CK076359
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|33815680|gb|CF333691.1|CF333691
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88314674|gb|CI606742.1|CI606742
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88725675|gb|CI748934.1|CI748934
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88575843|gb|CI669988.1|CI669988
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATGGGATTCTCCTGAGATGAAATCCACCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|58588133|gb|CF986441.1|CF986441
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88401847|gb|CI591174.1|CI591174
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88331273|gb|CI639684.1|CI639684
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|58692806|gb|CK081493.1|CK081493
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|88330299|gb|CI658610.1|CI658610
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCT
EST: gi|9457296|gb|AU063064.2|AU063064
EST:     AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC                         GTTGCTGAAAAGA
genomic: AAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGA

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), 75 (downstream exon)
Score: 116

ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttg ... aaactgttagGTTGCTGAAAAGATTGGATTTTCCTGAGATGAAATTCAGCTTGTATTTTCTTGGTTATGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTCgtaagttttgtcccttatcttcatcatataatgtacagttctgtatagcgtaaaacattaccacctcatgtgttctctcatgttaattaaagcatcgatg

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