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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGTGGATGTTCTTGATGAGAAACTCCAGAATGCTAGAACACTTGGAGCAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtattttttaactgtcaagttttcttagctacttaaccaccagcagttcaaaaacaactcgaattctgtttttaatttcccgttgctgatcttaatatgctatttcccgtcttcttcaagtgtccatcttgaaaatttcccattgaatgtgattatttgaatatcttactggctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g01760.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G024303_T01 (Zea mays), 5'ss of exon 6
TGCAGTGGATGTTCTTGATGAGAAACTCCAGAATGCTAGAACACTTGGAGCAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtattttttaa-ctgtcaagttttcttagctac---ttaaccaccagcagttcaaaaacaactcgaattctgtttttaatttcccgttgctgatcttaatatgctatttccc-------gtcttcttcaagtgtccatcttgaaaatttc--ccattgaatgtgattatt------tgaatatcttactggctgcag
|||||||||||| ||||||||||| || ||||| |||| |||||||||||||||||| ||||||||||| |||||||| ||||||||||||| ||| ||||||| | | || |||||||  ||| | | |||    | ||   |    |||      | |  || | |||  |        |  | ||||| |||||  | | || ||||         |   | |  || ||| ||| | |||  || |  | ||  | ||  | ||||      |||||  ||| |||    |||
TGCAGTGGATGTCCTTGATGAGAAGCTTCAGAACGCTACAACACTTGGAGCAACCCACACTGTAAATGCAGCAAAAGATGATGCAGTTGAAAGGATAAAGgtatgtctcaaactgtcaaagtttgtaatctatcaatgaagttcagaaagtaattctatatatctacttcattacaagtcctgtcattgcttatcttgtttttctttttcttcaagtgggctgtgtcaaaatgtgcatatggaactttccagctatgtattgatactattcagatgtgaatgccttgctgttcacag
















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|88976898|gb|CI257594.1|CI257594
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|88907686|gb|CI091084.1|CI091084
EST:     AAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: AAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|86502042|gb|CI144675.1|CI144675
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|88197083|gb|CI196933.1|CI196933
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|44674419|gb|CR287853.1|CR287853
EST:     CAACCCATACTGTAAATGCTGGAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACT
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACT
EST: gi|58682874|gb|CK071561.1|CK071561
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|88837935|gb|CI371513.1|CI371513
EST:     GTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTACCTGTGGAAGCACTTGTTAAG
genomic: GTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|86414410|gb|CI068813.1|CI068813
EST:     AAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: AAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|86503463|gb|CI146096.1|CI146096
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|86432655|gb|CI086266.1|CI086266
EST:     AAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: AAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|88833764|gb|CI077245.1|CI077245
EST:     CTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|58588843|gb|CF987151.1|CF987151
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|88903524|gb|CI089062.1|CI089062
EST:     ATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: ATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|94362588|gb|CI052707.1|CI052707
EST:     GAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: GAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
EST: gi|86497826|gb|CI140459.1|CI140459
EST:     CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAG                         GAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG
genomic: CAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAG

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: 73 (upstream exon), 75 (downstream exon)
Score: 65

TGCAGTGGATGTTCTTGATGAGAAACTCCAGAATGCTAGAACACTTGGAGCAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtatttttta ... ctggctgcagGAAATTACTGATGGGAGGGGTGTGGATGTAGCTGTGGAAGCACTTGGTAAGGCATTGACATTTTCTCAGTGCGCCAAAAGTGTACGAGATGGAGGCAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGTGGATGTTCTTGATGAGAAACTCCAGAATGCTAGAACACTTGGAGCAACCCATACTGTAAATGCTGCAAAAGAAGATGCAGTTGAAAAGATTAAGgtattttttaactgtcaagttttcttagctacttaaccaccagcagttcaaaaacaactcgaattctgtttttaatttcccgttgctgatcttaatatgctatttcccgtcttcttcaagtgtccatcttgaaaatttcccattgaatgtgattatttgaatatcttactggctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG