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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaataaaagttttccaattatgtgatgattatttaaactaaatagcagcagcacatgttttgcacccaaccgactttgaataaaccatcttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT

Basic information

species Oryza sativa
transcript LOC_Os01g01800.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01800.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 16
----ctaataaaagttttccaattatgtgatgattatttaaactaaatagcagcagcacatgttttgcacccaaccgactttgaataaaccatcttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAA--CTACCT----
      |   |  |  | |  | ||  |      ||   ||  ||| |   |  || |  || ||||||     |  | |||||  || ||| |||  ||||||||||||||||||||||||||||||||||||| ||||| | ||| |||||  | ||||||||||||  | | ||    
ttttggacggagggagtacggagtacctatatgctagacaa--taagttata-tagtagctgctttgcataatccgtaatttgagcaa-ccaactttgatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT
















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|86437315|gb|CI119037.1|CI119037
EST:     GGGGAAATTGTAAGGTTTTACGCTAATGATCAAAGAAAAATTACTTGCG                         ATCCTGAAACAAAGGGGCTTATTAAGAGAACTCTTGAAACTGGTCATGTAT
genomic: GGGGAAATTGTAAGGTTTTACGCTAATGATCAAAGAAAAATTACTTGCGgtgagtatat ... ttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTAT
EST: gi|29628866|gb|CB633877.1|CB633877
EST:     GGGGAAATTGTAAGGTTTTACGCTAATGATCAAAGAAAAATTACTTGCG                         ATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTAT
genomic: GGGGAAATTGTAAGGTTTTACGCTAATGATCAAAGAAAAATTACTTGCGgtgagtatat ... ttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTAT
EST: gi|32947857|gb|BP184429.1|BP184429
EST:     CGCTAATGATCAAAGAAAAATTACTTGCG                         ATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTAT
genomic: CGCTAATGATCAAAGAAAAATTACTTGCGgtgagtatat ... ttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 48 (upstream exon), 66 (downstream exon)
Score: 12

GGGGAAATTGTAAGGTTTTACGCTAATGATCAAAGAAAAATTACTTGCGgtgagtatat ... ttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcagcacatgttttgcacccaaccgactttgaataaaccatcttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT
                                        ccatcttc  CT-rich tract
                              tttgaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaataaaagttttccaattatgtgatgattatttaaactaaatagcagcagcacatgttttgcacccaaccgactttgaataaaccatcttcaatgcagATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- aataaaa
- - - - - - - - - - -tgtgatg
- - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - cagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaa