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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatctctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC

Basic information

species Zea mays
transcript GRMZM2G373175_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 7
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatc-tctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
||| | ||| || || | | || |    ||||        |||||||| |  | ||| |||  ||| ||||||||   |||||| |  || |  || | ||| ||||  ||||||||||||| || |||||||||||||| ||||| || || |||||||| |||||||| |||||||||||||| || ||||||||||||||||| |||||
gtatcagatccatccttcaaatcatccgtttatc-----actgctttatt--gaatcatcttgagcatttgtagc--atgtgctaactatacccacggattggcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 8
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatctctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcatttt-cagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
     || || |||      ||||   |    ||| | |      |||||    || |      ||| |  ||  |     |  ||| |       |  ||||| ||  ||||  |  ||||| | ||||||||  | ||||| ||  | || ||||||||||| ||||| | ||| || ||||| ||||||||||||||||| || ||| |
---gttggttgacc------atta---tccggcatgaaaatctgcttactgattattttc----cttataaagtataaagcccaatagt-----tggtctgtcaattgacagGGCACAACTTGACAATGCTTCCCATGGAACCCAAACTTGGCAAGATGCTTATATTTGGTGTTATCTTCAATTGCCTGGATCCCATATTAACTATTGTTGC

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 16
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatctctg---tagcttttgtagcttgtgtgctgataatgcttact---gcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
                             ||   | |   || ||   |   | |  | ||   || |||||     |    || |||  |    || |   || |   |||  ||||      | || | ||||||||  | ||||| ||  | || |||||||| || || || |||||||| ||||| |||||||||||||||||  | ||| |
----------------------------gttggttgatcccttctagtcctggaaaatttggcttatcttttcctcttgaaatgatgaagacttgtatttgggccttcaattgacagGGCGCTGCCTGACAATGCTTCCTATGGAACCCAAACTTGGCAAGATGCTAATATTAGGTGCTATTTTCAATTGCCTGGATCCCATATTAACTGTGGTTGC

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|37416592|gb|CF645948.1|CF645948
EST:     TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTG                         GAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA
genomic: TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA
EST: gi|6021234|gb|AW066162.1|AW066162
EST:     TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTG                         GAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA
genomic: TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
                                tgcttac  putative branch site (score: 2)
                                             tcattttc  putative PPT
         ttttgta  TA-rich tract