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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgaattcagatttttcactgcaccaacaagaaaaaccattatgtgaattcatgagtacactaacatctccaatgctccatttctttgtgaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG

Basic information

species Oryza sativa
transcript LOC_Os03g42220.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 13
gctgaattcagatttt---tcactgcaccaacaagaaaaaccattatgtgaattcatgagtacact-aacatctccaatgctccatttctt-tgtgaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG
 || | |    ||| |   |||||||  ||| |   | ||||||| | |   || ||||  | | | ||| ||||||   ||  |||  |  ||| ||| | ||||||||||||||||| | |||||||| ||| |  |||||||  | | ||||||||||||||||||||||| ||
act-agtatgcattctagatcactgctgcaa-agctacaaccattgttt---tttatgatgagattcaacgtctccagcacttaattcatcctgtaaaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAG

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 4
gctgaattcagatttttcactgcaccaacaagaaaaaccatta--tgtgaattcatga-gtacactaacatctccaatgctccatttctttgtgaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG
  || |||| |   | |    |||| |  || |   |   |          ||  ||  |  |   ||  || | | || |  |||  |||   ||| | ||||||||||||||||| | |||||||| ||||| ||||||||  | |  |||||||||||||||||||||| ||
--tgtattctggactct-ggagcactactaatattcattctagatcactgctttgtggtgagcttcaatgtcacgagtggttaattcattttgtaaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG
















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|58684862|gb|CK073549.1|CK073549
EST:     GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAG                         GTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
genomic: GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAGgtaattctca ... gaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
EST: gi|29676853|gb|CB673128.1|CB673128
EST:     GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAG                         GTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
genomic: GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAGgtaattctca ... gaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
EST: gi|29657046|gb|CB653321.1|CB653321
EST:     GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAG                         GTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
genomic: GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAGgtaattctca ... gaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
EST: gi|29616345|gb|CB621357.1|CB621357
EST:     GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAG                         GTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
genomic: GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAGgtaattctca ... gaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
EST: gi|88422879|gb|CI615179.1|CI615179
EST:     GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAG                         GTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA
genomic: GGCTGAAAAGTTAGTTAACATGAAAATTCATCCAATGACTATAATTGCAGgtaattctca ... gaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattcatgagtacactaacatctccaatgctccatttctttgtgaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG
              cactaac  putative branch site (score: 1)
                                   atttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgaattcagatttttcactgcaccaacaagaaaaaccattatgtgaattcatgagtacactaacatctccaatgctccatttctttgtgaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA