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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccttcatgattcctttttgtaatcatctagacctgcaacatgtattgtctattaagctataaactatttggatgtgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGCTGAAAGAAGTTTGCATAGATGGGCTCTTGATGATCTCCAGAGAATTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g66240.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66240.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G007160_T02 (Zea mays), 3'ss of exon 11
gtaaatccttcatgattcctttttgtaatcatctagacctgcaacatgtattgtctattaagctataaactatttggatgtgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGCTGAAAGAAGTTTGCATAGATGGGCTCTTGATGATCTCCAGAGAATTCAT
||||||| |    ||| ||  || |  |||||| | |     ||  | | |||| |    |     |  ||  |        || |||||| |||||||||||||||||||||||||||||||||||||||| || ||||||||| |||||||||||||||||||||| || || ||||| |||||| ||
gtaaatcttcagcgatgccagtt-gagatcatcaaaa----gaaagtatgttgtgtgactaatggaatgctgct--------ccattcagGAGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTTCTAAAAGCTGAACGAAGTTTGCATAGATGGGCTCTCGAAGACCTCCAAAGAATTTAT

upper sequence: LOC_Os01g66240.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 11
----------gtaaatccttcatgattcctttttgtaatca-tctagacctgcaacatgtattgtctattaagctataaactatttggatgtgccgttca--gGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGCTGAAAGAAGTTTGCATAGATGGGCTCTTGATGATCTCCAGAGAATTCAT
           ||  | ||     |||   ||||| ||| | |||   | | ||  |   |||||   | || | |  ||   |||     | | |||||  ||   ||||| ||  |||||||  | || || ||| | || ||  | ||||| |||||||| || ||||||||||||||||| ||||| ||| | || |||
aggttcaatgatatgtgctatcacatttaattttgaaatgaatctttccatacagaag--attgtgcttgaaaccaataatggtttatgc-ttctgttcatagGAAAATTGTTGAAGATGTACCTCGTGGGGTGCATGTGAACTTTTTGAAAGCAGAAAGAAGCTTACATAGATGGGCTCTTGAAGATCTTCAGCGGATCCAT
















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|33800785|gb|CF326264.1|CF326264
EST:     ATGAAGAGACTAACTTATG                         GGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
genomic: ATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
EST: gi|88849992|gb|CI091287.1|CI091287
EST:     CATGTACAAGTCCTATGAAGAGACTAACTTATG                         GGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
genomic: CATGTACAAGTCCTATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
EST: gi|29678812|gb|CB675087.1|CB675087
EST:     CTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATG                         GGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
genomic: CTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
EST: gi|3767332|gb|AU031442.1|AU031442
EST:     ACATGTACAAGTCCTATGAAGAGACTCACTTATG                         GGGGATTNTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
genomic: ACATGTACAAGTCCTATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
EST: gi|8858056|gb|AU095374.1|AU095374
EST:     CTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATG                         GGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
genomic: CTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
EST: gi|88980867|gb|CI022557.1|CI022557
EST:     CTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATG                         GGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC
genomic: CTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGC

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: 63 (upstream exon), 50 (downstream exon)
Score: 11

GCAGTCCATTAGGGTCACTATCGTCTTCAAGCTTCTCATGGATTTTTGACCTAAATGGCATATCTGACATGTACAAGTCCTATGAAGAGACTAACTTATGgtaaatcctt ... tgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGCTGAAAGAAGTTTGCATAGATGGGCTCTTGATGATCTCCAGAGAATTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctgcaacatgtattgtctattaagctataaactatttggatgtgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGCTGAAAGAAGTTTGCATAGATGGGCTCTTGATGATCTCCAGAGAATTCAT
                    tattaagctataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatccttcatgattcctttttgtaatcatctagacctgcaacatgtattgtctattaagctataaactatttggatgtgccgttcagGGGGATTGTAGAGAATGTACCAAGGGGTGTTCATATTAATTTCCTTAAAGCTGAAAGAAGTTTGCATAGATGGGCTCTTGATGATCTCCAGAGAATTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT