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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA

Basic information

species Oryza sativa
transcript LOC_Os08g23810.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 1
gtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA
||| || ||||  ||| ||  ||  |||  |      ||||  |   |||  |  |  ||  |    | ||| ||  |||||| |  ||||||||| ||||||||||||||||| || |||||||||||||||||||||||||| ||
gtatgttgatcagacttttaaagatttctttg-----cattggtcacttt--tgctgatccattgtcttatgtagtattctactttgacagGCACTTAACATATTTGAGACAAGTCTGAGGCGTGGAAAGTTTGATGAATCACGGAA

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 3
gtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA
||| || ||||  |||||| |||  |||  |      ||||      |||  |  |  ||  |    | ||| ||  |||| | |  ||||||||| ||||||||||||||||| || |||||||||||||||||||||||||| ||
gtatgttgatcagactcttacagatttctttg-----cattgaacacttt--tgctgatcgattgtcttatgtagtattcttctttgacagGCACTTAACATATTTGAGACAAGTCTGAGGCGTGGAAAGTTTGATGAATCACGGAA

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------gtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatgga-gagttctacctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA
                                                                            |    | |   |||| | | |    | || |    ||  ||||    |    |    || || || ||| |    | |  |||  |  | |||| || || || |||||| | |||||| |||||||||||||||| ||||||||   
gtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgacttttggaacaacacctcccccctccagtgcatat-gttttccagtccttttacggtgatacatttactaactgtgaactatttctatagGCTCTGAATATTTTTGAGTCCAGCCTACGGCGTGGAAAGTTTGACGAATCACGCGT

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaagtggatccaactcttgcagtgttcaatagggatcattttt--ttttttcctctttgtcattcacttaatggagagttctacctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA
             | |    ||  | |  |  | |  || |  |  ||  | | |      | ||       |   | ||| | |||  || ||  | ||   ||||| | ||||| ||||| || |||||| ||||||| |||||||||||||||||   
gtaagtaaattaatgatcacatatatcattctctgctttaatcacagagtaatctgagccatgtcaaaccattggattactaactgggaagctc--cttgtgtagGCATTGAACATTTTTGAAACCAGCCTACGGCGTGGGAAGTTTGATGAATCACGCGT

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|58686263|gb|CK074950.1|CK074950
EST:     GGTGCTGAAA-TC-TGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: GGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|58679709|gb|CK068396.1|CK068396
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|29613728|gb|CB618741.1|CB618741
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|58672850|gb|CK061536.1|CK061536
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTG
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTG
EST: gi|58659884|gb|CK048564.1|CK048564
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAAGGCGTGGAAAGTTTGATGAATC
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAA-GGCGTGGAAAGTTTGATGAATC
EST: gi|571922|gb|D41433.1|D41433
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|571926|gb|D41437.1|D41437
EST:     GGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGGTGCCT                         GCACTAAACATATTTGAGACAAGNCTAAGGCGTGGAAAGTTTGATGAATC
genomic: GGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGG-TGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATC
EST: gi|58656775|gb|CK045455.1|CK045455
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
EST: gi|33691058|gb|CF319297.1|CF319297
EST:     AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCT                         GCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA
genomic: AGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggat ... acctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacagGCACTAAACATATTTGAGACAAGCCTAAGGCGTGGAAAGTTTGATGAATCACGAAA
                            acttaat  putative branch site (score: 4)
                                         ttctacct  putative PPT
     ttttttttt  TA-rich tract