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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG

Basic information

species Zea mays
transcript GRMZM2G083716_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 8
--------------gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG
              | |||    ||   |||  | ||||  ||    |    |    ||||        ||||   |   |||||||  | | ||||||||||| || ||||||||||| || ||||||||||||||||||||||| || ||||||||||| |||||||| |||||||||
tttctctattatgaggctgtatattgaatgtgttgtttgtacaagaaaagaaaagcatcagtcctgctcctga--ttgcttttttatctatccaatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAGCTTGCTGGTGGTGTTGCAGTCATTCAG

upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 8
gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG
    |  | | ||       |||          | |  | || |    ||  |   |||     |   | | ||    |    || |||| || |||||||| ||||||||||||||||| |||||||| || || ||  |  | |||||||||||||| ||||||
----gtacatctcaaaaaacattgaaatgtcccaataaattggttttatgttacggtga----ttaagtctttgggtttg---tgtagGCTGCTGAACAAGACTATGAAAAGGAAAAGCTTAATGAGAGAATTGCTAAATTATCAGGCGGTGTTGCTGTAATTCAG

upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 7
gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG
           | |   ||||| |  ||||||   |  ||||   |  ||     ||       |||  |         ||| ||||||||||||| || || |||||||| || ||||| ||||| || || || || ||| | || ||||||||||||||||||
----------gtgcatatctatatagtcacttttttcgactgtctat-tgtgttgctagtctcttgtgatggatgtatgaatatgcagGCAGCAGATCAGGACTATGAAAAAGAGAAGCTTAATGAAAGAATTGCAAAACTTTCAGGTGGTGTTGCTGTCATTCAG

upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 8
------gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatt-tgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG
       |||| ||| |  ||     |    | ||           ||     |   || | ||  | ||| || |||   |  |  |  | ||||||||||| ||||||||||| |||||||| || ||||| || || || ||  |  | || ||||||||||| ||||||
gtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatct-ttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG

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|211389169|gb|FL356628.1|FL356628
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCNGCAGAACAAGAATNCGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAN
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|211390791|gb|FL311861.1|FL311861
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|211283747|gb|FL354677.1|FL354677
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|33094001|gb|CF053995.1|CF053995
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTGATTGAG                         GCAGCAGAACAAGAATACGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|22545503|gb|BU097862.1|BU097862
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|87156784|gb|DY401573.1|DY401573
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|32935129|gb|CF039941.1|CF039941
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTGATTGAG                         GCAGCAGAACAAGAATA
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATA
EST: gi|24934364|gb|CA452582.1|CA452582
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|23357758|gb|BU645407.1|BU645407
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|32837828|gb|CD977506.1|CD977506
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTGATTGAG                         GCAGCAGAACAAGAATACGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|211420404|gb|FL361813.1|FL361813
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTC
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTC
EST: gi|51592649|gb|CV071795.1|CV071795
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAGCAAGAATACGAAAAGGAAAAGCTCAATGAGAGGGATAGCGAA
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGG-ATAGCGAA
EST: gi|211414113|gb|FL317428.1|FL317428
EST:     CCCAGGAAGAAGTTACTAAGAGGGNTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCANTGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|211268071|gb|FL357474.1|FL357474
EST:     AAAAATCTCATTGAG                         GCAGCAGAACAAGAATACGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: AAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|26558604|gb|CA830839.1|CA830839
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|22545873|gb|BU098247.1|BU098247
EST:     CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: CCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
EST: gi|120480889|gb|EH211078.1|EH211078
EST:     AAAATCTCATTGAG                         GCAGCAGAACCAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG
genomic: AAAATCTCATTGAGgtctgacctt ... taatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG
                                          acctaat  putative branch site (score: 3)
                                 tttttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT