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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaataaccccattccaatttagcaatcaacatatttgggaattgagcatattaagagtatattccttggcattgacatccttttggttgatgtcaattaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g59920.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G133359_T02 (Zea mays), 3'ss of exon 5
-------gtaagttcaataaccccattc-------caatttagcaatcaacatatttgggaattga-gcatattaagagtatattccttggcattgacatc--cttttggttgatgtcaattaa-aacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
|| | | | |||| || ||||| | | ||||||| | || || | || |||| | | | ||||||| | |||||| || || ||| ||| |||| || ||||||||| |||||||| ||||||||||| ||| || ||||||| |||||||||
gtaatgcgttaactgcttgccccctttgtaataagcaattcaactttcaacatgctaggaaacaaaagcttattgaatatcttttccttgcctctgacatatactgtttgttcatgccaataaacaacagGTTACATTCCAAGTATATTAGATGTGCAGTTGATTGATGAGGTTGTGAAG
















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|58687991|gb|CK076678.1|CK076678
EST:     GCTGAAACTAGTGTAATCTCTGGTGATAATGCTG                         GTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
genomic: GCTGAAACTAGTGTAATCTCTGGTGATAATGCTGgtaagttcaa ... attaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
EST: gi|29683918|gb|CB680193.1|CB680193
EST:     TATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTG                         GTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATG
genomic: TATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTGgtaagttcaa ... attaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATG
EST: gi|58689817|gb|CK078504.1|CK078504
EST:     TATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTG                         GTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
genomic: TATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTGgtaagttcaa ... attaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
EST: gi|29683919|gb|CB680194.1|CB680194
EST:     TATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTG                         GTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
genomic: TATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTGgtaagttcaa ... attaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG

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: 67 (upstream exon), 44 (downstream exon)
Score: 6

GTTATTGGGGTAGAACCTGCTGAAACTAGTGTAATCTCTGGTGATAATGCTGgtaagttcaa ... attaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagagtatattccttggcattgacatccttttggttgatgtcaattaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG
                                          tcaattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcaataaccccattccaatttagcaatcaacatatttgggaattgagcatattaagagtatattccttggcattgacatccttttggttgatgtcaattaaaacagGTTATATTCCAAGCATATTAGATGTTCAGCTGCTTGATGAAGTTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT