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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT

Basic information

species Zea mays
transcript GRMZM2G000645_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
-ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
  || |   |   |    |  |     ||    ||  |   | | || | | | || | || | |  ||||| | | || || ||| ||||| ||||||||||||| ||||||||||| |||||| | || || || || ||||||||||| || | |||||||||||||||  |||| ||||||||||| |||||||| |
ggctacaacatttcttttctttctactaggtaatgttagttg-tttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
-------ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
         ||    |        || |   |  |  ||    | | |   |     ||||   |    ||     ||||||||   | ||    ||  |||  ||||  || ||||| || || |||||  |||| |||||||||||||||||||| |||||||| || || |||||  |||| ||||| ||||| |||||||| |
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgg----gtggtggctgattgt---tgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
------ccttccctagacccca-cccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
         |    | ||   |  || |   |  |  ||    | |    |     || |||||    ||  | |  | |||||   | ||    || ||||  ||||  || ||||| || || |||||  |||| |||||||| ||||||||||| |||||||| || || |||||  |||| ||||| ||||| |||||||| |
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaa--caatatttgtttcatgggtg-gtgactt-attgt---tgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtc----agAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
        | |  |||||| |   |       |  ||||   | |    ||||||||   |||| | |   |  | ||| |  | ||||   ||  |     |||| || | ||| || || |||||  |||| |||||||| ||||||||||| ||||| || || || ||||   |||| ||||| |||||||||||||| |
-taaaataataatccacccct-tagttttaattatcaccacttat-ttattttttcatgcatgt-tgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgat-tgtgagtaatcattttggttggt---cagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
   |    |      | |    |   ||  |     |     ||  |  ||||||    |   | |   ||| | | ||| |  | ||||   ||  |   |||||  | | ||| || || |||||  ||||||||||||| ||||||||||| || || || || || |||||  |||| ||||| |||||||||||||| |
agctttaaaataataatctgccccttagttttaattatt---tccactttttttttta-agcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 3'ss of exon 11
------------ccttccctagaccccacccatgcggaagcctctggcaccgggtct---gcccttttttcagta-atgtataatctgatt-gtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
             | |   ||||    |   |||        | |   |    |||    |    |  | ||| | |  |||    ||  |      ||   ||| |   |  ||||||||||||||| |||||||||||  |||| || || || || || ||||| ||||||||||| || |||||  |||| |||||                 
atttgaaatgaagcgttaatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagCTATTCTAACTC-TCAGAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGA----------------

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
--ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcc-cttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
   ||    |       |   |||        ||    |     | ||   ||     | || || |||  |   ||| |   ||||  ||||| ||  ||||||||||||||| |||||||||||  |||| || || || ||||||||||| ||||| || || || |||||| |||| ||| | ||||| |||||||| |
ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatt--taatt-ttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcaccgggtct---gcccttttttcagta-atgtataatctgatt-gtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
       ||||    |   |||        | |   |    |||    |    |  | ||| | |  |||    ||  |      ||   ||| |   |  ||||||||||||||| |||||||||||  |||| || || || || || ||||| ||||||||||| || |||||  |||| ||||| |||||||| |||||||
----taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
ccttccctagaccccacccatgcggaagcctctggcac---cgggtctgcccttttttcagta-atgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
     | |  | |          |   |  ||   ||        | |    || |||  ||  |  | || |       |   |  |  |||| ||   ||||||| | || |||||||| |||||  |||| |||||||| ||||||||||| |||||||| || ||||| ||  |||| ||||||||||| || ||||| |
----gcattaagctaggatgaatgattgtttccaccatattttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 11
--ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatc-tgattgtgagtaatcat-tttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
    | |   ||     |||    |  ||     |     | |  ||       | ||| | ||  ||| || ||  |||| ||  |  | | | ||||  ||||||||| ||||||| ||||||||  | || || || ||||| || ||||| |||||||| ||||||||||||||||| |||||||| ||||| ||||| |
gaggtgcttgaggtgtaacctggtcataa----ttattgtctgtgcttgaaacatgtcaattataaatattcatggatgtgtgtgtttgtgtcttgttgtgcagAGCTTGGAGCATAATCCTAATGGCAGATTTGTGGTCGTATGCGGTGATGGAGAGTACATTATTTATACTGCCCTGGCATGGAGGAACAGATCTTTTGGCT

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|26457397|gb|CA828980.1|CA828980
EST:     GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG                         AGCTTGAAGCATAACCCTAATGGACGGTTCGTTGT
genomic: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGT
EST: gi|32865242|gb|CF004924.1|CF004924
EST:     GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG                         AGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
genomic: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
EST: gi|31353243|gb|CD437600.1|CD437600
EST:     GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG                         AGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC
genomic: GATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAGgtacttctgg ... ggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
                      atctgat  putative branch site (score: 4)
             taatgtataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA