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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

Basic information

species Oryza sativa
transcript LOC_Os06g05180.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 5
gtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
|| |||||||| || || | ||| | |||    |  | |    | || | ||||   ||||||| ||    |||| | ||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||||
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctattaatttctctgactaacaaatag--cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
gtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
|| |||||||| || || | ||| | |||    |  | |    |||| | ||||   ||||||| ||    |||| | ||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| 
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatag--cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
gtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
|| |||||||| || || | ||| | |||    |  | |    |||| | ||||   ||||||| ||    |||| | ||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||||
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatag--cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
gtgtgttttcttgataatactgcctgcttatt--------gtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
||| | |||||  | || | ||  | |||  |         |||| |||| | ||||   ||||||||||    |||| | |||| |||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | |||| ||||||||| |||||| |||||||||||
gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataag-cttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
----gtgtgttttct--tgataatactgcctgctt---attgtc-tggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
    |||    ||||  |   | || |    | ||   ||||   |  | |||| | |||        ||   ||| || |  |||||| ||||| |||||| | ||| | || |||||||||||||||||||||||||||||||| ||| | ||| | || ||||| ||| ||||||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
--gtgtgttttcttgataatactgcctgcttattgtct-ggtgttgaattcttgaac-taacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
    |||  |   || |  | |    | |  | | |||   ||  | | || |||   |    ||  | | ||  | |||||| ||||| |||||  ||||| | ||||||||||| |||||||||||||| |||||||| ||| | ||| | || ||||| ||| ||||||| || || 
gtaagtggatcaatggtt-tgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttact-cagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
----gtgtgttttct--tgataatactgcctgctt---attgtc-tggtgttga--attcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
    |||    ||||  |   | || |    | ||   ||||   |  | ||||  ||| ||    | |   ||| || || |  |||||| ||||| |||||| | ||| | || |||||||||||||||||||||||||||||||| ||| | ||| | || ||||||||| | ||||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaattgtttttct--cagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
------gtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatt---tttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
         ||||||  || ||  | |||   |  | ||| | ||    || |     |||    | |    ||| |  || |||||| || || ||||| |||||| | |||||||||||||||||||| |||||||||||||| ||| | ||||  || |||||  | ||||| || || || 
gtaagcagatgttttactgttatgattgctaac--aatgttttgt----aacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
--gtgtgttttcttgataa----------tactgcctgcttattgt----ctggtgt-tgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
  | |||   | |||  |           |   |  || || ||||    ||    | |  ||| || |  |    | |  || |   |||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  | ||||| || |||||  ||||||| || || || 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
--------------gtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
              | |       |    ||| ||| |||||| |  ||| ||  |  ||   | || | |  ||| ||   |  |||||||| ||||| || || |||||||| | |||||||||||||||||||||||| |||||||| ||  || ||||||||| ||| |||||||| |  || || 
gtgagggagcttgggagctgcacttctgcaat-ctgactgcttttgttcttgtaattgatc--taaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

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|58690875|gb|CK079562.1|CK079562
EST:     GGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA                         TGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGT
genomic: GGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttc ... cttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGT




















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), 67 (downstream exon)
Score: 31

GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttc ... cttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
                              aactaac  putative branch site (score: 31)
                                        tttttcttgtt  putative PPT
                              aactaacatattttt  TA-rich tract