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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgaaacatcttatagtttccttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT

Basic information

species Oryza sativa
transcript LOC_Os06g46450.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G483889_T02 (Zea mays), 3'ss of exon 8
gtttgtgaaacatcttatagtttccttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT----------
||||||| ||||| |  ||  ||||||    || |||||   |  ||||  |   || || | |||| ||| |  |  | |||||| ||| ||||  | | |||||||| ||||||||||||| || || ||||| ||| ||||||||||||| ||||||||||||||||| ||||||||  || |||| || |||          
gtttgtggaacatttctta--ttccttt---ttcttgaattca--tttccatgcaagttatttctgtaaacttggcgataacttagctaatttgg--tacatgcagGGTCTAGCCTTCCAGTTAATTGATGATGTACTTAATTTCACAGGCACCTCTGCATCCCTTGGGAACGGTTCATTGTCTCATATTCGCCATGTGAGAATAA

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G483889_T01 (Zea mays), 3'ss of exon 9
gtttgtgaaacatcttatagtttccttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
||||||| ||||| |  ||  ||||||    || |||||   |  ||||  |   || || | |||| ||| |  |  | |||||| ||| ||||  | | |||||||| ||||||||||||| || || ||||| ||| ||||||||||||| ||||||||||||||||| ||||||||  || |||| || |||
gtttgtggaacatttctta--ttccttt---ttcttgaattca--tttccatgcaagttatttctgtaaacttggcgataacttagctaatttgg--tacatgcagGGTCTAGCCTTCCAGTTAATTGATGATGTACTTAATTTCACAGGCACCTCTGCATCCCTTGGGAACGGTTCATTGTCTCATATTCGCCAT

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G014508_T03 (Zea mays), 3'ss of exon 9
gtttgtgaaacatcttatagtttccttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
|||||| |||||||||| | || || | || ||| |  |  |  |||   ||   ||||| | |||| ||| |        ||||||||| ||||  | | |||||||| ||||||||||||| || || ||||||||||||||||| ||||| ||||||||||||||||||||||||||  ||||||| || || 
gtttgtaaaacatcttacatttcccgttccttttcttgaattc-attaacttgcaagctatttctgttaacttggtgacatcttagttaatttgg--tgcatgcagGGTCTAGCCTTCCAGTTAATTGATGATGTTCTTGATTTCACCGGCACCTCTGCATCCCTTGGGAAGGGTTCATTGTCTGATATTCGCCAC

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G18160.2 (Glycine max), 3'ss of exon 9
gtttgtgaaacatcttatagtttccttcccatttttgaagctagatttctttctta-gctaatgct-gtgaaccttccagtgacttagttaacttgggatc--cttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
         ||| | |||||||    ||  |||||     ||  |  |  |   || | |  || |  ||||  | |  |  | ||| ||  ||    |     ||||||||||| || || || ||||| || ||||||||||||||||||||||| || || |||||||| |||||||| ||| | || || ||||||
---------acaacatatagttaatatct-attttcctgtctgtacatgctatatatgtttttgtttatgaatttccttgaaatttatttccctctccactgttttgcagGGTTTGGCATTTCAATTGATAGATGATGTTCTTGATTTCACAGGCACATCAGCTTCCCTTGGAAAGGGTTCTTTATCAGACATTCGTCAT

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA05G21570.1 (Glycine max), 3'ss of exon 9
gtttgtgaaacatcttatagtttccttcccatttttgaa-gctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatc--cttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
       | | |  | |||  |   ||||  | | |  | | ||  |    |   |  ||  |  | ||||  | |  |  | ||| ||  ||    |     ||||||||||| || || || ||||| || ||||| ||||||||||||||||| || || |||||||| |||||||| ||| | || || ||||||
-------atatagttaatatctattttcctgtctgtacatgttatgtacagtatgtttctgtt--tatgaatttccttgaaatttatttccctctccactgttttgcagGGTTTGGCATTTCAATTGATAGATGATGTGCTTGATTTCACAGGCACATCAGCTTCCCTTGGAAAGGGTTCTTTATCAGACATTCGTCAT

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv06s0009g03090.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtgaaacatcttatagtttcc-ttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
     |||   ||  |  ||      ||    || ||     | | |||||||||||  |    || | || ||    |       | |  | |    ||    ||||| || || ||||| || || || || || ||||||||||||||||| || || ||||| ||||||||||||||  |||| |||||  ||
-----tgatttattgtggagaagatattggtgttgtttgttgtggttttctttctta--tgtctctttcaatctgattggtctggtgctgcccttttttctggacagGGATTGGCATTCCAATTAATAGATGACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGCAAT

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv00s0283g00050.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtgaaacatcttatagtttcc-ttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
     |||   ||  |  ||      ||    || ||     | | |||||||||||  |    || | || ||    |       | |  |||    ||    ||||| || || ||||| || || || || || ||||||||||||||||| || || ||||| ||||||||||||||  |||| |||||  ||
-----tgatttattgtggagaagatattggtgttgtttgctgtggttttctttctta--tgtctctttcaatctgattggtctggtgctgcctttttttctggacagGGATTGGCATTCCAATTAATAGATGACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGCAAT

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv15s0024g00850.t01 (Vitis vinifera), 3'ss of exon 9
gtttgtgaaacatcttatagtttcc-ttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
     |||   ||  |  ||      ||    || ||     | | |||||||||||  |    || | || ||    |       | |  | |    ||    ||||| || || ||||| || || || || || ||||||||||||||||| || || ||||| ||||||||||||||  |||| ||||| |||
-----tgatttattgtggagaagatattggtgttgtttgctgtggttttctttctta--tgtctctttcaatctgattggtctggtgctgcccttttttctggacagGGATTGGCATTCCAATTAATAGATGACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGCCAT

upper sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv03s0132g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtgaaacatcttatagtttcc-ttcccatttttgaagctagatttctttcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
     |||   ||  |  ||      ||    || ||     | | |||||||||||  |    || | || ||    |       | |  | |    ||    ||||| || || ||||| || || ||  | || ||||||||||||||||| || || ||||| ||||||||||||||  |||| |||||| ||
-----tgatttattgtggagaagatattggtgttgtttgctgtggttttctttctta--tgtctctttcaatctgattggtctggtgctgcccttttttctggacagGGATTGGCATTCCAATTAATAGATAACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGTAAT

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|58662085|gb|CK050765.1|CK050765
EST:     GGCACACTGCTGATGTGTCGATGCTCGCATATGAATATGGTCGAAACCTG                         GGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTC
genomic: GGCACACTGCTGATGTGTCAATGCTCGCATATGAATATGGTCGAAACCTGgtttgtgaaa ... atccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTC
EST: gi|29683022|gb|CB679297.1|CB679297
EST:     GGCACACTGCTGATGTGTCAATGCTCGCATATGAATATGGTCGAAACCTG                         GGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCT
genomic: GGCACACTGCTGATGTGTCAATGCTCGCATATGAATATGGTCGAAACCTGgtttgtgaaa ... atccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCT
EST: gi|24468700|gb|CA305649.1|CA305649
EST:     GGCACACTGCTGATGTGTCAATGCTCGCATATGAATATGGTCGAAACCTG                         GGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCT
genomic: GGCACACTGCTGATGTGTCAATGCTCGCATATGAATATGGTCGAAACCTGgtttgtgaaa ... atccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCT

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: 51 (upstream exon), 67 (downstream exon)
Score: 5

AACAGCATCATTGATATCAAATAGCTGCAAGGCTGTCGCTATTCTTGCAGGGCACACTGCTGATGTGTCAATGCTCGCATATGAATATGGTCGAAACCTGgtttgtgaaa ... atccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttagctaatgctgtgaaccttccagtgacttagttaacttgggatccttgcagGGTTTAGCCTTCCAGTTGATCGACGATGTTCTTGATTTCACAGGCACTTCTGCATCCCTTGGGAAGGGTTCATTAACTGATATCCGTCAT
                                 agttaac  putative branch site (score: 5)
                                              tccttgc  putative PPT
                               ttagttaa  TA-rich tract