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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA

Basic information

species Zea mays
transcript GRMZM2G180720_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 4
--tattattttggattgatgttaggatctaatgatagtg-atattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaat-ttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
  |||| | || ||| ||| |||  |  || | | || | ||     | |||    |||| | || |||||||      | | ||    |||||||| || ||||||| |||||||||||||||| |||||||||||||| ||||||||||| ||||||||||| ||| ||||||||||||||||||| |||||||||||||| 
tatattgtatttgat-gat-ttacaacatact-acagcgtatgcagcaacacttgagtattt-tattgatattacttaaattttggggatgttgaatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTACATGTCTCTGGATGAGATTTCTCCATTGACATTTAGCATTGGCAATACG

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G28460.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------tattattttggattgatgt-taggatctaatgatagtgatattatatcacgactgtatgta-tactgat--attttccctaatgtgttactgttga-atttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
                                                  |  ||||   |||| |||     || | ||| |  ||     | || |     ||  ||  || | ||  | | |   ||| |  |   | ||||   || ||||||| | ||||| |||||||| ||||||||| | || || || ||  | |||| |||||| |||||||||||||| || ||||| |||||||| || |||
gtaagcatatttttgtaattttttactgttagtttttgaattggttcaacaagatttcttattgttgtgctttatttcatgttgttgg-gccaaattaacttagtgggttctatttatcaaatgttgttaacgaatggattttgatgcttgtagGTGGGTAGCTGCTCAGAGCGTCTTCTACCACCTGTACAATCAAGTCCCATACACGTCTCTTGATCAGATTTCTCCCTTAACATTTAGCATTGGAAACACA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 4
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaa-tgtgttactgttgaatttata-----gGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
       |||  |||    | |  |  |       |  | | |      |  | |     |    ||||| |  |||| ||| |  |||   | | || |     ||||| | ||||| || || || ||||| ||  |||| || || ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| || || 
-----gattgagttgtctgttgttttcatcctctatcttttgagtctgagcttctgctcttctcaatattatgactaaatgtatggctgacaattgtacacaacaGGTGGGTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCGTACATGTCTCTGGATCAGATCTCTCCCTTGACGTTTAGCATTGGAAACAC-

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 4
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaa-tgtgttactgttgaatttata-----gGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
      ||  |||||    | |     |       |  | | ||     |  | |   | |    ||||| |  |||| ||| |   || | | |||| |     ||||| | ||||| || || || ||||| ||  |||| || || ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| || || 
------ttctgattgtctgttgttctcatcctctatattttgattctgagcttctgcttttctcaatattatgactaaatgtatggttggtaattttacacaacagGTGGCTAGCTGCTCAAAGTGTATTCTATCATCTATACAATCAAGTGTCATACATGTCTCTGGATCAGATCTCTCCTTTGACGTTTAGCATTGGAAACACC

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 3
-----tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
       |  ||||   ||    ||      |||  |     |    |  | | | ||   | ||||      | ||  ||||||  ||  || ||  |||| |||||| | ||||| ||||| || ||||||||||| || || || || || ||||||||||| |||||||||||||| || |||||||||||||| || |||
aattcagtctttttttcttttccttcttccttaaccac--ccacccaaccttatgtctccctttataaaatgttgttaactaatggatt-ttgatg--tttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCACTTGTACAATCAAGTCTCATACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATTGGAAACACA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G45840.1 (Glycine max), 3'ss of exon 4
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatg-tgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
 | || | ||  ||  |  |    ||   |||   |   |  |  |   |  | | | | |  ||  |||   | ||  | || ||||  || |   | |||||| | || || || ||| | || || ||  | || || || ||||| ||||||||||| ||| |||| ||||| |||||||| |||||||| || || 
gagtaatctgattttcttgtcttttcacttgaggttctgaaaaacttctgcgtttctttgtcttgtaattaaacatatggctgctacttgtgcaca-acagGTGGGTGGCAGCTCAAAGCATATTTTATCATCTGTACAATCAAGTGTCGTACATGTCTCTGGATGAGATCTCTCCCTTGACATTTAGCATTGGAAACACC

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------tattattttggattgatgt---taggatctaatgatagtg----atattatatcac--gactgtatgtatactgatatt-ttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
                                                  |  ||||   |||| |||   |   || | ||| |  ||    | ||||  | |   || | | | ||| |  || || ||  ||||||  ||  || ||  ||| ||||||| | ||||||||||| || || |||||||| || || || || || ||||||||||| |||||||||||||| || ||||| |||||||| || |||
gtaagcacatttttttaattttttactgttagtttttgaattggttcaacaagatttcttattgttgtgctttttatttcatgttgttgggccaaattaacttagtggattctgtttat-caaatgttgttaactaatggatt-ttgatg--tttgtagGTGGGTAGCTGCACAGAGTGTCTTTTACCACTTGTACAATCAAGTCTCATACATGTCTCTTGATCAGATTTCTCCCTTAACATTTAGCATTGGAAACACA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 3
--tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaattt-atagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
    | ||||  ||||| ||  | |    ||    | | |  || |    | | ||| |  | | | |    ||   |||    |   | || | ||| | |||||| | ||||| ||||| || ||||||||  | || || || || || ||||||||||| |||||||||||||| || ||||||||||| || || |||
ctggtcatttgtgattgctgccaag--tcaaaaccaatcactttcttcatcaaatgttta-acattaaatcattaattaactactgggttttaatttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCATCTGTACAATCAAGTCTCTTACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATAGGGAACACA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 4
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
                                             || |   |  |||| |  ||||    |  |   |   |||   || |    |||||        || | |||    | |      ||  | || ||   | | |||||   |  |  | |  ||   | |  |   |  |  ||||| |||    
--------------------------------------------gtctc--ttacatgtctcttgatcagatttc---tcccttaacattcagC--ATAGGGAACACAATGAAGAGAATTCGGTAATTGTCTCTTCTATCCTTATCTTCTACACACCAATTCAGCCCATCAATGCTCTTGGAGCCGCCATTG-CAA----

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------tattattttggattgatgttaggat---ctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
                                                                                                     |    |||| | | ||    || ||    | | |||| ||| | |  | || ||  ||  |  |      | |     |  ||    |  ||||  | | ||||||| | |  || ||||| || ||||||||||| || ||||||||||| |||||||| ||  |  ||||||| ||| |||| |||||||||||||| || 
gtagctgcatctattagttttcctgttactactagaacgtaaactgtattgttggtgcggtttttagtatgtgagcttgtgcatgagctttccccaggtggtgaagttttcggtcgagtagagaatgcgttgaggataatgagagtggagcatgagggtcaggttttaaccaatccgtttggtg----atggttg--tgtgtagGTGGGTGGTGGCGCAGAGTGTATTCTACCACTTGTACAACCAGGTGTCATACATGTCGCTGAACGAGATTTCGCCACTGACCTTCAGCATTGGCAACACC

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------tattattttggattgatgttaggatctaatgatagtgata-----ttatatca-cgactgt-atgtatactgatattttccctaatgtgtta-----ctgttgaatt-tatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
                                             ||| ||  ||  | ||  ||||| |   | |  || |      ||| || | ||| | | | | ||   | |||||   | | |   | |       ||||     |  |||||| | |  |||||||| ||||||||||||||||| ||||| ||||| ||||||||  | ||  | || || ||| | ||||||||| ||||||| || 
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgc-aggatatcgcggtgttgctgcgggtttacatgagcgaatattacgaatgacggtatttaagcaagttgataagaaaatggttgtgcgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ35859 (Selaginella moellendorffii), 3'ss of exon 3
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
             | | ||| |   ||    |   ||| | | |  |    | ||     | ||    || |  || | |   | | ||    |    |||||| |    ||||||||||| ||||||||||| || ||||| || || || ||||| || || ||||| |||||  |||| ||||||||||| || || 
------------gtaacgttggtcacttccaaacttgagactctgccttccccgt---cgttct----ttctttctcacgccgt-ccgtctgctaaccagGTGGGTGATCGCACAGAGCGTCTTCTACCACTTGTACAACCAAGTCTCGTATATGTCGCTGGACCAGATATCTCCGCTGACTTTCAGCATTGGTAACACC

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|67042737|gb|CO468992.1|CO468992
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGNTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
EST: gi|211127527|gb|FL066343.1|FL066343
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
EST: gi|33102249|gb|CF062209.1|CF062209
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
EST: gi|211127528|gb|FL066344.1|FL066344
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAAAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCCAGGTGTCCC
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACC-AGGTGTCC-
EST: gi|4647070|gb|AI622145.1|AI622145
EST:     GCTGCTGGTTGGCAAAAGGTTCTTGCANAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCNCAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
EST: gi|211128448|gb|FL066345.1|FL066345
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
EST: gi|211039688|gb|FL176199.1|FL176199
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
EST: gi|5030714|gb|AI714908.1|AI714908
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTG                         GTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaaga ... gaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA
             tatactgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattattttggattgatgttaggatctaatgatagtgatattatatcacgactgtatgtatactgatattttccctaatgtgttactgttgaatttatagGTGGATTGCTGCACAGAGCGTGTTCTACCACTTATATAACCAGGTGTCCTACATGTCTCTCGATCAGATTTCTCCATTGACATTCAGCATTGGCAATACA

- - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttact