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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT

Basic information

species Oryza sativa
transcript LOC_Os02g47220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
------------------------------------------gtaac-tttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                                           ||||  ||| || |     |   | | ||  | |  || || ||  |   |    || ||| ||||||||||  |||||||||||||||| || |||||||| |||||||||||||||||||| |||||||| ||||| ||||||
gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------gtaactttcatattgacttactat---ttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                                              |  | | |  |  ||  | |||   |||||||| |  ||| |||||  |  |     |||||  |||||||||  |||||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||||
gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatttttgtcttacaacat-----gtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
----gtaactttcatattgacttactatttttaggtcacctttttct--tatcaagtatgtt----gtcttt---------------gcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
    |||  | |   |    | |    ||  ||   | |  |||| |  | |||| ||| ||    || |||                ||| | |||  | ||||||||||||||||| || || || |||||||| ||| | || || ||||| |||| ||||||||||
gtgagtatttgttgcagaagcctgaagttactatacccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 1
---------------------gtaactttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                       || || | ||| | |   ||  |||   || |  ||||| |  | || |    ||    | ||| | |||  | ||||||||||||||||| |||||||| |||||||| ||| | ||||| ||||| ||||  |||||||||
gtgatttctttctctttttgcagaagttac-tatagtcccccttgtttattgttagttttttttattaaaattacctgcaaatacagGTACAAGTTAATTAAGGAAGTTGGTGATGGGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 1
----------------gtaactttcatattgac-ttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                | ||||| | | || |  ||  |||||| | ||     | |   |   |  | ||  | || | ||| |  |  || || |||||||||||||| |||||||| || ||||| ||||| || |||||||| || | ||||||||||
gtgagtgggcttgtatggaacttgcttgttaatatttgtattttaatgtgttgatatgtctgagagttttg--gcctctacagGTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTT

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|58610974|gb|CK038686.1|CK038686
EST:     CATTGACCGGCATAATGGACAG                         ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: CATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
EST: gi|58662505|gb|CK051191.1|CK051191
EST:     CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAG                         ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
EST: gi|29625051|gb|CB630062.1|CB630062
EST:     CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAG                         ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
EST: gi|88839102|gb|CI378026.1|CI378026
EST:     ACATTAACCGCCATAATGGACAC                         ATTCAAAATGATTAAGGAAATTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: ACATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
EST: gi|58664681|gb|CK053367.1|CK053367
EST:     CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAG                         ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
EST: gi|58670491|gb|CK059177.1|CK059177
EST:     CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAG                         ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
EST: gi|58665074|gb|CK053760.1|CK053760
EST:     CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAG                         ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG
genomic: CAACAGGAAAAGGCTAGCACAAGGCTGACATTGACCGGCATAATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
   gacttac  putative branch site (score: 2)
                                           ttgtcttt  putative PPT
      ttactattttta  TA-rich tract