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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcttaataccatggatgattgcaatttctaaaagctggaaagcactatttaccagcttattgtttgtatcaatgcaaaatcatttaattcaacatcatcatctgtatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGAACAGAGATTGAAAGACTTGAAGGATGAGGATGTCACAGACCGTTTTCCT

Basic information

species Oryza sativa
transcript LOC_Os09g39660.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39660.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G142502_T03 (Zea mays), 3'ss of exon 8
gttagtgcttaataccatggatg-attgcaatttctaaaagctggaaagcactatttac-cagcttattgtttgtatcaatgcaaaatcattt-----aattca----------------acatcatcatctgtatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGAACAGAGATTGAAAGACTTGAAGGATGAGGATGTCACAGACCGTTTTCCT
      | |    || |||  || | |  |      ||||||| | || |  | |  |   | |||| |  |||||| ||| ||  |||||||     ||||                  | ||  || ||| |||||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||| || | |||||||||||||  ||||  |  |  |||
------gttagccactatgcgtgcactatataactcaaaagctagcaaaccatgtcgagataacttaattattgtataaatacaccatcattttttaaaattttgaggtggaatcggtttaaattttcttctatatcttgaagGCAAGCCGAACTGATGGAAAGGAAGCGGATGAAGAAACTTAGGCAGAAAGAACAGAGGTTAAAAAACCTCAAGGATGAGGATGCGACAGTTCAGTCACCT
















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|88672246|gb|CI726362.1|CI726362
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88593902|gb|CI713856.1|CI713856
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88668495|gb|CI722057.1|CI722057
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88674647|gb|CI728760.1|CI728760
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCACGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|89173145|gb|CI720975.1|CI720975
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88673485|gb|CI727598.1|CI727598
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88667994|gb|CI722733.1|CI722733
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88674685|gb|CI728798.1|CI728798
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|44671112|gb|CR284546.1|CR284546
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
EST: gi|88676076|gb|CI730189.1|CI730189
EST:     TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAG                         GCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA
genomic: TTAAGATGCCAGAAGTTGCTCGTGGAGGAAGAGGAAGCTGCTCAGAAAAGgttagtgctt ... tatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttgtatcaatgcaaaatcatttaattcaacatcatcatctgtatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGAACAGAGATTGAAAGACTTGAAGGATGAGGATGTCACAGACCGTTTTCCT
                      atttaat  putative branch site (score: 4)
                aaaatcatttaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgcttaataccatggatgattgcaatttctaaaagctggaaagcactatttaccagcttattgtttgtatcaatgcaaaatcatttaattcaacatcatcatctgtatcttgaagGCAAGCTGAACTGATAGAAAGGAAACGGATGAAGAAACTGAGGCAGAAAGAACAGAGATTGAAAGACTTGAAGGATGAGGATGTCACAGACCGTTTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG