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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatgtaatgtaccaaaatggtggtctgacactttatttatgtacattagagcatggccattaattttgtggctgtaactattacttggttgctcagtctatggttttttattttgtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAATAATGCTTGTTGAACTAAAGAAGCTGATTGAAGCTAATCCCTTGTTCCGT

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G030422_T01 (Zea mays), 3'ss of exon 4
gtatgaatgtaatgtaccaaaatggtggtctgacactttatttatgtacattagagcatggccattaattttgtggctgt-aactattacttggttgctcagtctatggttttttattttgtct--tgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAATAATGCTTGTTGAACTAAAGAAGCTGATTGAAGCTAATCCCTTGTTCCGT
                  |||  | ||    | ||   |  || | |  ||    ||||   ||||| | |  ||||| | | || || ||   ||||||||    || ||| | |||||   |  |  ||||||||||||||| ||||| || || ||||||||||||||||| |||  ||||||||||| ||| || |||||||||||||||||||||||||||||||||
----------------gtaaagagctgactggccagccttgttttttgtat----gcat---cattattatcatggcttttagctgtttctgtattgctcagcgactgatttctgattttccttgttattagGGAAAATGAGCAGCTCTCGAAGTATGGTGATACAAAATCTGCAAGACAAATAATGCTTGCTGAGCTGAAGAAGCTGATTGAAGCTAATCCCTTGTTCCGT

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------gtatgaatgtaatgtaccaaaatggtggtctgacactttatttatgtacattagagcatggccat-taattttgtg----gctgtaactattacttggttgctcagtctatg--gttttttattttgt-cttgat--agGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAATAATGCTTGTTGAACTAAAGAAGCTGATTGAAGCTAATCCCTTGTTCCGT
                                                     |    ||| | |||   |   |||   |||    ||   ||||    |   |    | ||  | || | ||       |  ||| | |      |    ||||  |        | | |  || ||  ||| |  || ||||||||||| || || || ||||| ||||| ||||| ||||||   || |||||| | ||||| |||||||| || |||||||||||  | ||||| 
gtgaatgccttcgccagcacaatttcatgtgtgactgggggcctcatctcaccaaatgtgtgaagtattcag--ggtaacctgtacgttcgattatagtgaagtgtttgtagctctatagtgttacaagaagtcgtagccaaatgacgaaaactcaagcggccccactctgtgcttggtatttggtgcagAGAAAATGAGCAGCTGTCAAAGTACGGAGATACGAAATCCGCCAGAAACATTATGCTTCTAGAACTCAAGAAGCTTATAGAAGCTAATCCACTCTTCCGA
















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|29656775|gb|CB653050.1|CB653050
EST:     GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|29629469|gb|CB634478.1|CB634478
EST:     GAGGAATTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|27334445|gb|CA882896.1|CA882896
EST:     GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAAAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|88298806|gb|CI566003.1|CI566003
EST:     GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAA-TCTGCCAGAGCA-T
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|58652923|gb|CK041603.1|CK041603
EST:     GAGGAATTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|88426720|gb|CI584083.1|CI584083
EST:     GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|29656774|gb|CB653049.1|CB653049
EST:     GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
EST: gi|88717854|gb|CI739366.1|CI739366
EST:     GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAG                         GGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT
genomic: GAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACGTTGGAAAACTTTAGgtatgaatgt ... gtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctgtaactattacttggttgctcagtctatggttttttattttgtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAATAATGCTTGTTGAACTAAAGAAGCTGATTGAAGCTAATCCCTTGTTCCGT
  ctgtaac  putative branch site (score: 3)
                                  ttttttattttgtctt  putative PPT
                             tatggttttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatgtaatgtaccaaaatggtggtctgacactttatttatgtacattagagcatggccattaattttgtggctgtaactattacttggttgctcagtctatggttttttattttgtcttgatagGGAAAATGAGCAACTCTCCAAATACGGTGATACAAAATCTGCCAGAGCAATAATGCTTGTTGAACTAAAGAAGCTGATTGAAGCTAATCCCTTGTTCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC