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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaattattctgtttttaaatagcctatcatgaattgaaaatccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG

Basic information

species Oryza sativa
transcript LOC_Os06g20370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G465169_T01 (Zea mays), 3'ss of exon 7
gtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaattat--tctgtttttaaatagcct---atcatgaattgaaaat-ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG
||| |   ||| || |||   |||| |||||  || | |  | | ||| || | |  ||||| | |||| ||||||   ||     | | |  | |||| |   | ||  ||   ||||| ||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||| || ||||| |||||||||||||
gtatggcaataattggtt-cggcaagtcaaagttactgctgcatgtatcctgtaaccatttatgcgataataccaacgcatagctggctgtggagtagcttttaaccacaaaactaaaataccttctgcagGATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATCCTTGTTAACAAGATTCCAG

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G101874_T01 (Zea mays), 3'ss of exon 8
gtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaa-ttattctgttttta-aatagcct---atcatgaattgaaaat-ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG
||| ||  ||| || |||   |||| |||||| || | | |  | ||| || | || ||||  | |||| |||||||   || |||  | |  |  ||| |   | ||  || | ||||| ||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||| |||||||| |||||||||||||
gtatgacaataattggtt-cggcaagtcaaaattactgc-ttatgtatcctgtgatcatttgtgcgataataccaaagccatgctggctgtgcagcagcttttaaccacaaaattaaaataccttctgcagGATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAG

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 7
gtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaattattctgtttttaaatagcctatcatgaattgaaaatccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG
           ||| ||| ||||          |  | ||   | |  ||||| |    ||   | ||  | |  | ||    | |  ||  | |  ||  ||  |  |   ||        |||||||| ||||| |||||  ||||| ||||||| ||| | || ||||||||||| || || ||||||||  | |||||||| |||||||
-----------tttagttttagctt--------tgctgcaaggtatgatctttaaatggttgcctaatcctcctcatttggattataattttacactctgacacaaccttgtaaa------acagGATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGTGCAGAGAAAGCTCGGATATTGGTCAACAAAATTCCAG

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaattattctgtttttaaatagcctatcatgaattgaaaatccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG
||| | | | |||  | | |   ||   |||   |||||   | |||  | |  |   || || ||||        ||| || ||  |||        | |  || |   ||||        |||||| | ||||| ||||   ||||||||||||| ||  ||||||||||  | ||||| || ||||||||||| |||| ||||||| | |
gtatgctaacattg-gctatgttaa--taaacacattac--ttattaagcat--agagttcaattgatg-------attcttttgggttt-------ttgttctgga---aaaa--------cagGATCAGAACAGGTATAGTGCAAGCCGAGGTGCGCATTTGAATCTCAAGAGAGCTGAGAAAGCTCGGATTCTGGTCAGCAAGATTACTG

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S153_95V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaagatgatattttgttgtagcaaatcaaaagtattacatcttttattctttcatgatttaagtgatattaccaaattattctgtttttaaatagcctatcatga-attgaaaatccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG
                               ||  ||||  |||| |||    |||||  |  ||  | | |  | |   ||| ||  |   | |    |   ||| |  |    |  ||  ||||||||| ||  ||| |    | |||  |||||| ||||| ||||||||||||||||| |||||||||       ||   ||  ||||||
----------------------------gcgagctttac-cctttcatt----catgacctt-gtattttaaggacacatttccgtcctggtagaatgaaaattgacaaagttcttatttacgcagGATGAGAATCGATTTG---CTAGCAAAGGTGCTCACCTCAATCTCAAACGTGCTGAGAAGGCTCGGGCAGCGATCGCTAAACTTCCAG

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|66924847|gb|CX111695.1|CX111695
EST:     GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
genomic: GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
EST: gi|3760183|gb|C97441.1|C97441
EST:     GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
genomic: GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
EST: gi|88583042|gb|CI699517.1|CI699517
EST:     ATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         TATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
genomic: ATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
EST: gi|58668066|gb|CK056752.1|CK056752
EST:     GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
genomic: GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
EST: gi|218497048|gb|FG946045.1|FG946045
EST:     GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCCAACGT
genomic: GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
EST: gi|58597733|gb|CK008261.1|CK008261
EST:     GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
genomic: GATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
EST: gi|88586562|gb|CI704268.1|CI704268
EST:     ATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGG                         TATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT
genomic: ATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGT

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: 69 (upstream exon), 72 (downstream exon)
Score: 33

AGCAAAGGAAGAAGCATTGAGTAGAAAAGAAATATTAGACAAAGTTGAAAGATGGATGTCTGCTTGTGAAGAAGAAAGCTGGCTTGAAGATTATAACCGGgtaagatgat ... ccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaaattattctgtttttaaatagcctatcatgaattgaaaatccttctgcagGATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG
                                            tccttctgc  CT-rich tract
     aattattctgttttta  TA-rich tract