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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaagtaatggtgttattcatgttttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA

Basic information

species Oryza sativa
transcript LOC_Os06g36090.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
gtgagtt--ttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaagtaatggtgttattcatgt---tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
|| ||||  |||||  ||||  || || |  ||| | |||| |      |  || || |   | ||| |||| ||  | |    ||||||||||| ||||| | |||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||| || ||||||||  || |   ||
gttagttgtttcttcaatca--cctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 21
gtgagttttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaag-------taatggtgttattcatgttttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
|| |||| |  ||  |||| |    ||  ||   |  || | || | || | ||| |||        | ||| | ||  ||   |  | |||||||| |||||   |||||||||||||||||||||| |||||||| ||||||||||||||||||||||||| |||||||| || |||||||| ||| |  |||
gtcagttgt--tgtttcaatcaccatccctgcgatccttttcctacctgtaggattaaatagaggactcatgttttttctctattcctgtttcagAGAATTCCTGGATGGTGGATCTGGTACTACTGGATTTGCCCACTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGGAAGACCTCA

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
gtgagttttcttg-gatcaaaccgtttctttgaactttttattcttcttggaag----atcaaagtaatggtgttattcatgttt-tatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAA-ATCA
||||||    ||   ||       ||   |||||      ||   |     ||     |  ||  |||   |  ||   |  ||    |||||||  ||||| ||||||||| | ||||| |||||| |||| ||| |||||||||||||||||||  | || ||  | || ||| ||||  ||||  |  ||| 
gtgagtaccattctaatttcgttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC-

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
gtgagttttcttgga-tcaaaccgtttctttgaactttttattcttcttggaagatcaaagtaatggtgttattcatgtttta---tttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA-
||||||    ||  | |       |||  |||||      ||   |     ||     |   ||   | || | |    |||    |||||||  ||||| ||||||||| | ||||| |||||| |||| ||| |||||||||||||||||||  | || ||  | || ||| ||||  ||||   |  || 
gtgagtaccattccagtttcgtaattttattgaaacaagcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAG-GACCCAC

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
----------gtgagttttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaagta-atggtgttattcatgttttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
          || | |||||| | |  ||| |      |  |||  |  ||  ||||     |||   |  | | | || | ||  | |  | || ||||| ||||| ||||||||||| ||||| |||||| | || ||| |||| ||||| ||||||||  | || ||  | ||||| || ||| | ||  | |  |
gttagtgttggttacttttctggcaagaaagc------tgaaaccctaaatgattctctattgattctatcataagctggttttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv09s0002g03570.t01 (Vitis vinifera), 3'ss of exon 4
----gtgagttttcttggatcaaaccgtttctttga-acttttta------ttcttcttggaagatcaaagtaatggtgttattcatgtttta--tttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
    ||   ||||| |   |   |  |   |||| |  | ||  |       || ||    |  | | || | |       ||| |||||| |  |||||||  |||||||| ||||||||||||||||| ||| |||||||| | ||||||||||| || ||||| || ||  | || ||||||||| | ||  | |  |
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCACTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
----gtgagttttcttggatcaaaccgtttctttga-acttttta------ttcttcttggaagatcaaagtaatggtgttattcatgtttta--tttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
    ||   ||||| |   |   |  |   |||| |  | ||  |       || ||    |  | | || | |       ||| |||||| |  |||||||  |||||||| ||||||||||||||||| ||| |||||||| | ||||||||||| || ||||| || ||  | || ||||||||| | ||  | |  |
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

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|29643489|gb|CB648496.1|CB648496
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
EST: gi|88675207|gb|CI727322.1|CI727322
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGC
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGC
EST: gi|88671120|gb|CI725236.1|CI725236
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTA
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTA
EST: gi|88674502|gb|CI728615.1|CI728615
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCT
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCT
EST: gi|88668092|gb|CI722831.1|CI722831
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGAACA                         AGGATTCCCAAATGGTGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGG
EST: gi|29673479|gb|CB669754.1|CB669754
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
EST: gi|88908493|gb|CI713052.1|CI713052
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATG
EST: gi|38470736|gb|CF954867.1|CF954867
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
EST: gi|86260714|gb|CI000162.1|CI000162
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
EST: gi|88574669|gb|CI666438.1|CI666438
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
EST: gi|88904455|gb|CI711763.1|CI711763
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTG
EST: gi|157652524|gb|EX452158.1|EX452158
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTAC
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTAC
EST: gi|88985544|gb|CI003020.1|CI003020
EST:     CGTTCTATTCCTTGTCCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGAGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
EST: gi|33682388|gb|CF310627.1|CF310627
EST:     CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCA                         AGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG
genomic: CGTTCTATTCCTTGTTCAACCTATTCTCAGGATTCTTCATTCCGAGACCAgtgagttttc ... tttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttattcttcttggaagatcaaagtaatggtgttattcatgttttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
                                            ttttatttc  CT-rich tract
                                   ttattcatgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaagtaatggtgttattcatgttttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA