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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttattggcaactttaccaaattttggtaaggttgaaaatggcatcaaagtgaacaggcccatagtgtcggtcttaaactttggtgtgaaatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA

Basic information

species Oryza sativa
transcript LOC_Os03g20420.3
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20420.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G180889_T01 (Zea mays), 3'ss of exon 5
ctttattggcaactttaccaaattttggtaaggttgaaaatggcatcaaagtgaacaggcccatagtgtcggtcttaaactttggtgtgaaatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA
     || |  ||| |        ||| ||  ||  |       |  ||  | || | |   ||    ||    | ||    | ||||       || ||||||||||||||||||| || ||||||||||||||| || | |||||||| ||  || |  | |||||||| ||||| |||||||||||| ||||| |  
----gtttgatactgtg----gacttgatacagtgcatggcaa-actaagatcaatatggtgattacatc---ttgaattagttgtgttcgtgattatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATGGGTGTTATATTGAACTCGTACTCCCTGACCTCATTTGATCTCCTCTTGGACTCGG

upper sequence: LOC_Os03g20420.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G131440_T01 (Zea mays), 3'ss of exon 8
---ctttattggcaactttac-caaattttggtaaggttgaaaatggcatcaaagtgaacaggccc--atagtgtcg-gtcttaaactttggtgtgaaatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA
      ||||| | | || |  | |    ||| ||   | | |     |    | |||  |  ||   | |  || | ||  | |  | ||   |    ||||| ||||||||||||||||||| || ||||||||||||||| || | ||   | |  | |||||           |      |    |                 
gtttgatattgtcgatttgatacgacgcatggcaa--ctaagagcaatacggtaatgattaccccttgaaatagttgtgttgtgatgtctgaactcttgtgctatagGTGGTGCCGGCGGCAAGTCCAATAACCAACGCGGGCAAGCAAATTTCTATTTTGGTGGACGAGAGGCATGTTGTGGTGGCAAACTAA-------------
















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|22306425|gb|BQ907647.1|BQ907647
EST:     AACATCTGGTT-GCTCGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GT-GTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGCAGATGGGTGTC
genomic: TACATCTGGTTGGCT-GCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|55411122|gb|CV723498.1|CV723498
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|86528047|gb|CI168253.1|CI168253
EST:     CAGCCTGACAAG                         GTGGTTCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: CAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
EST: gi|29645169|gb|CB650176.1|CB650176
EST:     TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAG                         GTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC
genomic: TTACATCTGGTTGGCTGCGGGATGAGAACTCTTTCCAACAGCCTGACAAGgtttgctaca ... aatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagtgaacaggcccatagtgtcggtcttaaactttggtgtgaaatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA
                             ttaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttattggcaactttaccaaattttggtaaggttgaaaatggcatcaaagtgaacaggcccatagtgtcggtcttaaactttggtgtgaaatgctacagGTGGTGCCGGCGGCAAGCCCCATAACCAACGCGGGCGAGAAGATGGGTGTCATTGTGGATCCATACTCCCTCACCTCGTTTGATCTCCTCCTGGACACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - accaaat
- - - - - - - - - - - - - - - - - - - - - -catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caggccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg