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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgggacagacgtaacttagtgtatcattagttatattatagatacaatgtttgcatactagcctttttatcatgcgtaatcgccaacttattttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os12g32230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135816_T01 (Zea mays), 3'ss of exon 5
cgggacagacgtaacttagtgtatcattagttatattatagatacaatgtttgcatactagcc---tttttatcatgcgtaatcgcc--aacttattttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
   |    ||    | ||| |    | | |||  |    |     | ||| ||  ||||| ||   | |||| |     | ||  |   | ||   | |   |||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||| ||||| || || ||||||||||
---gttttaccgttcctaggg--ctaatggttggaggtcactgttattgtgtgggtactaaccaaatatttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG

upper sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
cgggacagacgtaacttagtgtatcattagttatattatagatacaatgtttgcatactagcc---tttttatcatgcgtaatcgcc--aacttattttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG---------------
   |    ||    | ||| |    | | |||  |    |     | ||| ||  ||||| ||   | |||| |     | ||  |   | ||   | |   |||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||| ||||| || || ||||||||||               
---gttttaccgttcctaggg--ctaatggttggaggtcactgttattgtgtgggtactaaccaaatatttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA

upper sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
cgggacagacgtaacttag---tgtatcattagttatattatagatacaatgtttgcatactagcctttttatcatgcgtaatcgccaacttattttaccc-agGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
   | || |    ||||     |||||    |  | || |  || ||   | | |||   || |   | | ||  | | ||||       || ||||  || |||| || ||||||||||||  ||| ||||| ||||| || || || ||||| |||||||| |||||||| || |||||||| | ||
---gtcatagactacttgaaattgtattgccaactttagttaagctatttt-tatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG

upper sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
cgggacagacgtaacttagtgtatcattagttatattatagatacaatgttt---gcatactagcctttttatcatgcgtaatcgccaacttattttaccc-agGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
   | || |    ||||    |   || ||  | | | ||| ||   | |||   |    || |   | | ||  | | ||||       ||  |||   | |||| || ||||||||||||  ||| ||||| |||||||| || || ||||| |||||||| || ||||| || |||||||| | ||
---gtcatagactacttgaaattgtataagc-aaactttagttaagctattttatggggtcttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG

upper sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G31955.1 (Arabidopsis thaliana), 3'ss of exon 5
cgggacagacgtaacttagtgtatcat-tagttatatta--tagatacaatgtttgcatactagcctttttatcatgcgtaatcgccaacttatttta---cccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG-----------
        | |||  |   ||  |||| |  || ||  |   ||  |  |  | |     ||    ||  | ||     | |     || | |   |      ||||| || || |||||||||  ||||||||| ||| |||| |||||||| ||||| |||||||| ||||| ||||||||||||| ||           
------gtaagtatttagttgcttcatctgattttacgaaccagtcaagaaatctttcctctgtttttcgtttctgtattgacttaaaattcacaatgggtttcagGTGAAGAGAAAGAAAGCTGCACACGCTGGAATGCTTGACATTGCTAAAACAGCTAATAGACCAATGATACACATTGGTGGCTAAGCTCCGGTGAAC

upper sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 7
cgggacaga-cgtaacttagtgtatcattagttatattatagata-caatgtttgcatactagcctttttatcatgcgtaatcgccaacttattttacc-cagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
 ||   ||| | |  |   |    ||| |  | |  ||  |  |  |  ||| ||     |  |   |   |  | | || |        |  ||  |  ||||| || ||||||||||||   || ||||| |||||||| ||||| ||||| |||||||| || ||||| || |||||||||| ||
-ggccaagatcattgccctgaaattcact--tcagctttcaagtgtccttgtctggtctttgcctaatacgtttttcatatttcttgttcttgttggctgcagGTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAG

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|86903275|gb|CI313638.1|CI313638
EST:     CCGAGCTGGTGTTGATGATCCTGGACTCAGAGAAAATAATAAGCGCTGCGG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGAC
genomic: CCGAGCTGGTGTTGATGATGCTGGACTCAGAG-AAATAATAAGCGCTGC-Ggtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGAC
EST: gi|58692671|gb|CK081358.1|CK081358
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
EST: gi|89166490|gb|CI103776.1|CI103776
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
EST: gi|29671509|gb|CB667784.1|CB667784
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
EST: gi|89163717|gb|CI100607.1|CI100607
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
EST: gi|29639063|gb|CB644072.1|CB644072
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
EST: gi|88223338|gb|CI223187.1|CI223187
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
EST: gi|218504356|gb|FG958785.1|FG958785
EST:     TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA
genomic: TCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACA

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: 65 (upstream exon), 49 (downstream exon)
Score: 15

GTGAGCTTGAGAGAGCCTATCCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtaagtgtag ... ttttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtttgcatactagcctttttatcatgcgtaatcgccaacttattttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
                                         cttatttt  CT-rich tract
                                       aacttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgggacagacgtaacttagtgtatcattagttatattatagatacaatgtttgcatactagcctttttatcatgcgtaatcgccaacttattttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - gtgtatc
- - - - - - - - - - - - - - - - - - - - gatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcatac