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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_Os06g05180.1
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






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA
                              aactaac  putative branch site (score: 1)
                                        tttttcttgtt  putative PPT
                              aactaacatattttt  TA-rich tract