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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacaagtaaggcagtattaatgaacaatgaatagctatattatcttaaatggacatttctttgttatatatttatgtttttatctttctttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g43030.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43030.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 20
-----gcacaagtaaggcagtattaatgaacaatgaatagctatattatcttaaatggacatttctttgttatatatttatgtttttatctttctttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTG
        || |   |  ||||||| |  ||  | | | ||||  || |        |   |   |  | | || ||||  |     |||  ||| || || |||||||| || ||||||||||| ||||||||| |||  || |||||||| |||||||||
gttgaaagcatgcgggttagtattattatact-taactcgctaatttgttgccttctgttgtacatcagcttta-attttcgca---atccatctatgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG
















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|87005314|gb|CI285536.1|CI285536
EST:     TTTCATTTGAACTCAACATGAGAAAACAAAAGATTTTACTTGCTTTTCAG                         GCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGT
genomic: TTTCATTTGAACTCAACATGAGAAAACAAAAGATTTTACTTGCTTTTCAGgtatttagtt ... ttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGT
EST: gi|33794849|gb|CF323303.1|CF323303
EST:     TTTCATTTGAACTCAACATGAGAAAACAAAAGATTTTACTTGCTTTTCAG                         GCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGT
genomic: TTTCATTTGAACTCAACATGAGAAAACAAAAGATTTTACTTGCTTTTCAGgtatttagtt ... ttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGT
EST: gi|58694649|gb|CK083336.1|CK083336
EST:     TTTCATTTGAACTCAACATGAGAAAACAAAAGATTTTACTTGCTTTTCAG                         GCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGT
genomic: TTTCATTTGAACTCAACATGAGAAAACAAAAGATTTTACTTGCTTTTCAGgtatttagtt ... ttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatggacatttctttgttatatatttatgtttttatctttctttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTG
                                           ctttgat  putative branch site (score: 5)
                          tttatgtttttatctt  CT-rich tract
          atttctttgttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacaagtaaggcagtattaatgaacaatgaatagctatattatcttaaatggacatttctttgttatatatttatgtttttatctttctttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA