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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcgtatattgtcaccatatttcaaatttcgtatgaatgagggatatataaccaacctcctgctatattatattactttgctgtaacctgatacaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAG

Basic information

species Oryza sativa
transcript LOC_Os08g25624.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 4
gttcgtatattgtcaccatatttcaaatttcgtatgaatgagggatatata-accaacctcctgctat--attatattactttgctg-taacctgat-acaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAG
    ||| | |   | |||  || || ||   | |||||          ||  ||    | |  ||||  | |||||||  ||| || ||   |||| | ||||||||||| |||||||||||||||||||||||||| ||||| || ||  | |||||  |||||||||| ||||||||||| || |||
----gtaaagttcaaacatggtt-aagttatctttgaatactttgccagtatgcctgagttccactatgaaatatattaacttgttggtagtttgatgaaaacagGGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG
















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|88575372|gb|CI669517.1|CI669517
EST:     ATTGTTGGTGGTGTAGCATTGGCATCTCTTACTGAGGCTTCCTTCAACTG                         GGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAA
genomic: ATTGTTGGTGGTGTAGCATTGGCATCTCTTACTGAGGCTTCCTTCAACTGgtatgtaaca ... gatacaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAA
EST: gi|58610772|gb|CK038484.1|CK038484
EST:     ATTGTTGGTGGTGTAGCATTGGCATCTCTTACTGAGGCTTCCTTCAACTG                         GGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAA
genomic: ATTGTTGGTGGTGTAGCATTGGCATCTCTTACTGAGGCTTCCTTCAACTGgtatgtaaca ... gatacaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAA
EST: gi|58688340|gb|CK077027.1|CK077027
EST:     GGTGGTGTAGCA-TGGCATCTCTTACTGAGGCTTCCTTCAACTG                         GGCTGGG-TTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAA
genomic: GGTGGTGTAGCATTGGCATCTCTTACTGAGGCTTCCTTCAACTGgtatgtaaca ... gatacaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatataaccaacctcctgctatattatattactttgctgtaacctgatacaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAG
                   tatattatattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtatattgtcaccatatttcaaatttcgtatgaatgagggatatataaccaacctcctgctatattatattactttgctgtaacctgatacaacagGGCTGGGTTTTGGAGTGCAATGGCTTCAAATGTCACCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - -atgaatg
- - - - - - - - - - - - - - - - - - - - - - - - -taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgt