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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggaaatgttatgttttcctaacagtggtcatatatctgccatatgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT

Basic information

species Oryza sativa
transcript LOC_Os01g67250.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G093119_T01 (Zea mays), 3'ss of exon 2
atggaaatgt-tatgttttcctaacagtggtcatatatctgccatatgtctttt--tttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
 ||  | ||| ||   |||  | | |||  |  | | |   | |    |  |    ||| | | ||| |||||| |  ||  ||  |   | ||  ||||||||||| || ||||||||||| ||||| ||||||||||| |||||||| ||||||||| | || |||||||| ||||||||||| ||||| |||||||||||
-tgacattgtgtagaatttaatgatagtattagtgtttggcctaacaattctgcaatttctataattctgagctgaaaatctatggttgctatt--cctgcagATTCTATCATATTCCCTGATGTTCCAATTGCACTTCGGTTATCAAGTCATCTTATGTTAGGCGTGGTCAGAATCTATTCTCGGAAGGTCAACTACCTATT

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G421829_T01 (Zea mays), 3'ss of exon 2
--atggaaat--gttat-gttttcctaacagtggtcatatatctgccatatgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
   | ||| |   | || || ||| |    |   | | |  |||||  | |   |||| |      |||  ||||| |  || |||  |   | |  |  ||||||||| || ||||||||||| ||||| || |||||||| |||||||| ||||||||| | || |||||||| ||||||||||| ||||| |||||||||||
gtgtagaatttaataatagtattcgtgtttggcctaacaattctgcactgtacattttcta---aaattcagagctgaaaatcaatggttgctatcct--tgcagATTCCATCATATTCCCTGACGTTCCAATCGCACTTCGGTTATCAAGTCATCTTATGTTAGGCGTGGTCAGAATCTATTCTCGGAAGGTCAACTACCTATT

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G38310.1 (Glycine max), 3'ss of exon 1
----atggaaatgttatgttttcctaacagtggtcatatatctgccatatgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
      | |  |  |||||   | |        |  | |||||   || |   |  | |||| |||| |    |||| |  || | |    | |     ||||||||| ||| | || |||||| | || || ||||| || || || ||||||||| | ||||||||||| ||||| |||||| | |||||||| ||||| ||
tccttcgtaggttgtatgtgaacgtgctgcatttgttgtatcta--attttgatcatattttgtcatctcatacttatt--tagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G48020.1 (Glycine max), 3'ss of exon 1
---atggaaatgttatgttttcctaacagtggtcatatatctgccatatgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
    || |  |  || ||   | |  | |   |      | |   || |   |  | |||| |||| |    |||| |  || | |   || |       ||||||| ||| | ||||||||||| || |||||||| || || || ||||||||| | ||||||||||| ||||| |||||| | |||||||| ||||| ||
cctttgtaggttgtacgtgaacgtg-ctgcatttggtgttgtctaattttgatcatattttatcatctcatacttatt--tagtcaattttatgaatgaacagATTCCATTCTTTTCCCTGAAGTACCAATTGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGAAAGGTGAATTACCTTTT

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0220g00080.t01 (Vitis vinifera), 3'ss of exon 1
--atggaaatgttatgttttcctaacagtggtcatatatctgccatatgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
   |  |  | |  | | ||  | | |    ||||  || |   ||     | ||  |  |  |   ||  |   ||   | |  |  || |||  |  ||||||||||| | || ||||| || || |||||||| || || || ||||||||| |||| |||||||| ||||| |||||| | ||||| || ||||| ||
aacttcacttctgctttctttattatatatctcattaatttaaaatgcacttcttactcatctaacatgtacc--gttcaatttttttttctttctcaacagATTCAATTCTTTTTCCTGATGTACCAATTGCACTACGTTTGTCCAGCCATCTTCTGCTGGGTGTGGTGAGGATATATTCTAGAAAGGTTAATTACCTTTT

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|95101281|gb|CI693024.1|CI693024
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88576761|gb|CI673286.1|CI673286
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAC                         ATTCAATTATATTCCCTGAAGTTCCGATTGCANTTCGATCATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88583301|gb|CI700772.1|CI700772
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|29630217|gb|CB635226.1|CB635226
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88429094|gb|CI689974.1|CI689974
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCACGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88588063|gb|CI705856.1|CI705856
EST:     GAAGCTGCGGAACAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88381570|gb|CI682231.1|CI682231
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|29678404|gb|CB674679.1|CB674679
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
                             tattaat  putative branch site (score: 2)
                                      tcatttttttcctgc  putative PPT
     ttttttttttcatttt  TA-rich tract