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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaattgaccattcgatttcagttgctctttttacaaattgctctagactctaaacataatgagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAATACAATCGATTTGGGGGTTGCCCAAGAGAAGCTGGAAACCTACCAGGAC

Basic information

species Oryza sativa
transcript LOC_Os05g29050.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G066485_T02 (Zea mays), 3'ss of exon 17
gtatgaattgaccattcgatttcagttgctctttttacaaattgctctagactct-aaacataatgagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAATACAATCGATTTGGGGGTTGCCCAAGAGAAGCTGGAAACCTACCAGGAC------------------
||||||||| |    |  |||   |||||  ||| |   || |||| | | |||| ||||||   |  ||| |||||  ||||||||||| |||||||||||||  ||||| ||||| || |||| |||||| |||||||| ||||||||||||||||| ||| | ||||| ||                   
gtatgaatttaagcctacattggggttgcattttgtgtcaagtgctgtggtctctgaaacatttagtccattcagggttcaatttcggcaaagCTTTGCTCACTTGAGGGACAAAATTGGCCACACTACAATTGATTTGGGTGTTGCCCAAGAGAAGCTAGAAGCTTACCAAGAGGGTGATCTCAAAAGTATC

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 18
gtatgaattgaccattcgatttcagttgctctttttacaaattgctctagactct-aaacataatgagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAATACAATCGATTTGGGGGTTGCCCAAGAGAAGCTGGAAACCTACCAGGAC
||||||||| |    |  |||   |||||  ||| |   || |||| | | |||| ||||||   |  ||| |||||  ||||||||||| |||||||||||||  ||||| ||||| || |||| |||||| |||||||| ||||||||||||||||| ||| | ||||| || 
gtatgaatttaagcctacattggggttgcattttgtgtcaagtgctgtggtctctgaaacatttagtccattcagGGTTCAATTTCGGCAAAGCTTTGCTCACTTGAGGGACAAAATTGGCCACACTACAATTGATTTGGGTGTTGCCCAAGAGAAGCTAGAAGCTTACCAAGAG
















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|218495731|gb|FG952898.1|FG952898
EST:     ATTTACCAAGATGTCTTCTCATGTGTACCTACTGATCTTATCCATTCAAG                         GGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAG
genomic: ATTTACCAAGATGTCTTCTCATGTGTACCTAATGATCTTATCCATTCAAGgtatgaattg ... gagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAA
EST: gi|88508982|gb|CI436488.1|CI436488
EST:     ATTTACCAAGATGTCTTCTCATGTGTACCTAATGATCTTATCCATTCAAG                         GGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAA
genomic: ATTTACCAAGATGTCTTCTCATGTGTACCTAATGATCTTATCCATTCAAGgtatgaattg ... gagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAA
EST: gi|88488621|gb|CI425892.1|CI425892
EST:     ATTTACCAAGATGTCTTGTCATGTGTACCTAATGATCTTATCCATTCAAG                         GGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAA
genomic: ATTTACCAAGATGTCTTCTCATGTGTACCTAATGATCTTATCCATTCAAGgtatgaattg ... gagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagttgctctttttacaaattgctctagactctaaacataatgagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAATACAATCGATTTGGGGGTTGCCCAAGAGAAGCTGGAAACCTACCAGGAC
                                ctctaaa  putative branch site (score: 3)
          tctttttacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaattgaccattcgatttcagttgctctttttacaaattgctctagactctaaacataatgagcatgcagGGCCCAATTTCGGCAGAGCTTTGCTCACTGCAGGGATAAAATCGGTCACAATACAATCGATTTGGGGGTTGCCCAAGAGAAGCTGGAAACCTACCAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA