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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtgtctatatgtgctaaactccaaattcatgggaaactacaattccacttctaagtttttattactttcctcagattttgtttgattggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCCCGTGAGCAGTTAGAGAGGGGTGTCATCTGCTCCTCTGCTGGAAATCATG

Basic information

species Zea mays
transcript GRMZM2G155323_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155323_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g50510.1 (Oryza sativa), 3'ss of exon 1
-tttagtgtctatatgtgctaaactccaaattcatgggaaactacaattccacttctaagtttttattactttcctcagattttgtttgattggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCCCGTGAGCAGTTAGAGAGGGGTGTCATCTGCTCCTCTGCTGGAAATCATG
 ||   | ||| ||  |    |  |     |     |    ||   | | || ||   |||||| | |       |   |||||| ||  ||| |||  |||||||||| ||||||||| | ||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||| || ||||
attagttttctgtagctttacatatattgctcttctgacttctgacagtacaattggcagtttt-actggccagatataattttggttacttgttgtgtagGTATTCTCATTCAAGTTGAGAGGAGCATACAATATGATGGCAAAGCTCTCGCGTGAACAGTTGGAGAGGGGTGTCATCTGCTCCTCTGCTGGGAACCATG
















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|74234813|gb|DT642727.1|DT642727
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
EST: gi|22546336|gb|BU098647.1|BU098647
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
EST: gi|60338910|gb|DN205883.1|DN205883
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
EST: gi|22472274|gb|BU036754.1|BU036754
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
EST: gi|50324583|gb|CO519709.1|CO519709
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
EST: gi|60397382|gb|DN230198.1|DN230198
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
EST: gi|87156844|gb|DY401633.1|DY401633
EST:     CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCG                         GTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC
genomic: CCGATCGCCTTGGGGTCAACCTCTGGATCAAGCGCGAGGACCTGCAGCCGgtaatcgaca ... tggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccacttctaagtttttattactttcctcagattttgtttgattggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCCCGTGAGCAGTTAGAGAGGGGTGTCATCTGCTCCTCTGCTGGAAATCATG
                                      gtttgat  putative branch site (score: 5)
          taagtttttattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagtgtctatatgtgctaaactccaaattcatgggaaactacaattccacttctaagtttttattactttcctcagattttgtttgattggtgtacagGTATTCTCGTTCAAGTTGCGGGGAGCATACAACATGATGGCAAAGCTCTCCCGTGAGCAGTTAGAGAGGGGTGTCATCTGCTCCTCTGCTGGAAATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - -tgtgcta
- - - - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - aactaca
- - - - - - - - - - - - - - - - - - - - - - - - ccacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg