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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctgaatgctgatcgacttttccttatggcttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA

Basic information

species Oryza sativa
transcript LOC_Os06g51029.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G126361_T01 (Zea mays), 3'ss of exon 1
---------ctttctgaatgctgatcgacttttccttatggcttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA
          |||   || |  | | || ||||||   |    |||  |||| |     |||||  ||||   |  |   || ||||||| | | || || ||  |||||| |||||  ||||||||||| |||| |||||||| || ||||| ||||||||  | || ||||||||||||||||| ||||| || |||||| | ||||
cacaatattatttaaaaaagaagtttgatttttcccagta---tcctgatttca-----ttttaaatgtatgtatacatgagcttacaagtc-tttttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 1
----ctttctgaatgctgatcgacttttccttatggc-ttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA
     ||| ||   |  | || ||  ||   |      || |    |||||    ||    |  |  | | |      || |  |    | || || |||   |||| || || |||||||| || || ||||| ||||| |||||||| ||||||||  ||||||||||||| |||||||| |||||||| || ||  ||||||
ggaagtttttg---gtaggtccacgcttgaatgcaatatttcttgattgattttgttgcgcccatttctatgtctggattaatcaac--tcttcttctctttcagGTGCATTCTAGAGGAAAAGCACTTGCAAAGGATGTTGACTTTGAAAAAATTGCAAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATCTGATGA

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 1
-ctttctgaatgctgatcgacttttccttatg-gcttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA
  ||  || ||  || | |        || |  ||        | |||    |||  |  ||||    | | |  |  |  |  ||   | || |||   |||| || || |||||||| || || ||||| ||||| || ||||| ||||||||  ||||||||||||| |||||||| |||||||| || || |||||||
gattggtgcat-ttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatca-actcttctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA

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|38473941|gb|CF958073.1|CF958073
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
EST: gi|11026064|gb|AU162665.1|AU162665
EST:     AGGTCACCGTAGACANGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTAACTCGAGAAGGAAAGGC
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGA-GGAAAGGC
EST: gi|313083957|gb|HO213740.1|HO213740
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
EST: gi|313079776|gb|HO213215.1|HO213215
EST:     AGGTCGCCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
EST: gi|25802953|gb|CA758914.1|CA758914
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
EST: gi|87017664|gb|CI289797.1|CI289797
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCT--GGCAAAAGATGTCGA
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGA
EST: gi|38470925|gb|CF955056.1|CF955056
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
EST: gi|38470079|gb|CF954210.1|CF954210
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
EST: gi|58608440|gb|CK036473.1|CK036473
EST:     AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAG                         GTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT
genomic: AGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATT

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), 72 (downstream exon)
Score: 58

GCCTGATGTGCTCGACGCGGCTCTTCTTCGCCCTGGGAGGTTCGATCGGCAGGTCACCGTAGACAGGCCGGATGTCGCCGGGCGTGTCAAGATTCTTGAGgtgagcactt ... tgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA
     ttttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttctgaatgctgatcgacttttccttatggcttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT