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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagtatatatacgtactgtactttttttatggacaactctactgaacatttagaagagcaaggattttgttaataaatatatgtttttcataaccatgttggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG

Basic information

species Zea mays
transcript GRMZM2G036861_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------gtgagtagtatatatacgtactgtactttttttatggacaactctactgaacatttagaagagcaaggattttgttaataaatatatgtttttcataaccatgttggt--ccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG
                                                                      |  |  | | |  | ||  | |   |    || || |  ||   | || |   ||| | | ||   |  |      || | ||  | | |    |||||||| ||  |  ||||||||| || ||||||| || || |  ||| ||||||| |||||||| ||||||||||||||||| |||||||||||||| || |||
gtaagtacctaagttttttcgcattaatgtattgaaatactacctccgtcccaaaatataacaacttttggctacgaatctggacacacaattgcccagattcatagctaaaaatgcttatattttgggacagagggagt------aacatattaaagctggaaataaccatattcattcccacagGATTACAGTGAAATGGCTAAGGCCTACAGACCTTCACATGCAGATGCAACTTATGACTTCAAATACGGTGTTAGAGCAGTGCAG

upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtagtatatatacgtactgtactttttttatggacaactctactgaacatttagaagagcaaggattttgttaataaatatatgtttttcataaccatgttggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG
     | || |   |  |   || | ||  ||| |   ||  | |        || ||    | || | ||| |   ||    | |  ||||| ||    || ||      |||||| |    |||||  |||| | |||  | ||||| |||||||| || ||||||||||||||||| ||||| ||  | || |||
--ctcttgtttccttgggctttgaatttagtttgtaaccatttgtctc-----ttcagttatgtaatg-tttagaagatcccaacaatttttttattggaatttt------cagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG

upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtagtatatatacgtactgtactttttttatggacaactctactgaacatttagaagagcaaggattttgttaataaatatatgtttttcataaccatgttggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG
       |||  |||   |      || | | | |      |||| ||  | || || |     | | ||  || | |   ||||         ||    |||    | | |||||| |  | ||  |  | |  |  ||| | |||||||||||||| ||||| ||||| |||||||| ||||| |||||  | |||
-------gtaagtatctctctctctctctctctctctctctctct-ctatatatatatatatata-gtatggtgcttaatcatattgaagagctatgttaatga-atttctcagGATTATAGCGAGCTGTCAAGGGCTTACAGGCCTTCTCATGCAGATGCAACCTATGATTTCAAGTATGGTGTAAGAGCAATCCAG

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|211106358|gb|FL258167.1|FL258167
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|211106359|gb|FL258168.1|FL258168
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|148952455|gb|EC898280.2|EC898280
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|148961384|gb|EE012122.2|EE012122
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|71442820|gb|DR823870.1|DR823870
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|148995329|gb|EE034551.2|EE034551
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|149036977|gb|EE155215.2|EE155215
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|148950790|gb|EC896395.2|EC896395
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAACCAATGTGTACCGAACTTCTCCTGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|149084565|gb|EE174034.2|EE174034
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|149078720|gb|EE167520.2|EE167520
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|76934911|gb|DV174083.1|DV174083
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCCCCGTGAAATAGCCAATGTGTACCGACCTTTTCATG
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATG
EST: gi|211106349|gb|FL258158.1|FL258158
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|148957149|gb|EC903140.2|EC903140
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|211106350|gb|FL258159.1|FL258159
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|71768469|gb|DR966406.1|DR966406
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|148947516|gb|EC892976.2|EC892976
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|78109644|gb|DV528060.1|DV528060
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACT
EST: gi|76281790|gb|DV021358.1|DV021358
EST:     CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGT                         GATCACCGTGAAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAAC
genomic: CTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAATAGGCAGTgtgagtagta ... tggtccacagGATCACCGTGAAA-TAGCCAATGTGTACCGACCTTCTCATGCAGACGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcaaggattttgttaataaatatatgtttttcataaccatgttggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG
                                 tcataac  putative branch site (score: 2)
     aaggattttgttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagtatatatacgtactgtactttttttatggacaactctactgaacatttagaagagcaaggattttgttaataaatatatgtttttcataaccatgttggtccacagGATCACCGTGAAATAGCCAATGTGTACCGACCTTCTCATGCAGACGCAACTTATGACTTCAAGTACGGTGTTAGAGCTGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT