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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG

Basic information

species Zea mays
transcript GRMZM2G480607_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
gtatgg-tcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG
||| || |||| | |||   ||||   | | | |||||||| ||   | |||  ||  | ||||       ||  ||| ||||| |||||  |       ||||| ||||||||||| ||||| | ||| ||||||||||| ||||| || ||||||||||||||||| ||||| ||||||||  ||||  | |||||||||
gtaagggtcaaatcctattacagtg--tgcataaatacatcataaccttttttttttctgttttct-----tatgtttcatgtttctgctaat------tagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG

upper sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G20750.1 (Glycine max), 3'ss of exon 3
-----------------------------gtatggtcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaa---taaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG
                             |    |    ||  |  | |  ||    |||||  | ||| ||| || ||   || || |||     | |   |||||||| ||||| |||  || ||   |||  |  | || |||||||| ||||| ||  |||| || || ||||| |||||||| ||||||||||| |||||||||||||| || ||  | ||| |  | 
gtaatagtctctcttatattttcctcactgagaagcttcctattgtaaccataaaa-cttgatgatatc-tacatttttggtttattgtttcgttctgagattaaattttgtgttgttgc--cttctttgcagACAGCTTAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTAGTTATGAAGCGTTCTCAGCCTAAAGTACTGCGCTTGAATTTGATT

upper sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
------------------gtatggtcaactgctaaatcagta-gtttcttgaatacatcctacgttctttcattgttatttt--tgctta------------ataaattttatgttgctg----ctgctgctgct-------cagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG
                   |||  |   ||     ||    | | |  |||| || ||| | | || ||   || || ||||  || |||            ||  | ||| ||||| ||     || || |||        |||  |  | || |||||||| ||||| ||  |||| || || ||||| |||||||| ||||||||||| ||||| |||||||| || ||  | ||| |  | 
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatc-tccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT

upper sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------------gtatggtcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG
                                                                                     | ||   | ||| |     | || |||||||  | || |     |    | ||| | |||  |  |   |   ||  | ||| ||  || |  ||  |||| |  | || |||||||| ||  | ||  |||||||||| || ||||||||||| ||||||||||| || || |||||||| || ||  | ||| | || 
gtaatatactctttctaatttttccataaaaatgtttttatttatttatttattttcatttccctcctgggaattcctttatttctctgtcaagctgttgt-ctattaatttcttgg-ttcagcagttatgtccttattttcattactcttcccttggttaaaagttacttgtgtta-tgtgcagGCAGCTCAAACATGAGGAAAAATGCTGCATGGAGGAGCTGCAATGCAACATTGTGGTTATGAAGCGCTCCCAACCTAAAGTTCTCCGCTTGAATTTGGTT

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|211362239|gb|FK992227.1|FK992227
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211362238|gb|FK992226.1|FK992226
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211364886|gb|FK992235.1|FK992235
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211362237|gb|FK992225.1|FK992225
EST:     TTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: TTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211364889|gb|FK992238.1|FK992238
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211174473|gb|FL037929.1|FL037929
EST:     GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211364885|gb|FK992234.1|FK992234
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211364887|gb|FK992236.1|FK992236
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211362242|gb|FK992230.1|FK992230
EST:     AGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211364884|gb|FK992233.1|FK992233
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211362243|gb|FK992231.1|FK992231
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211096511|gb|FL457291.1|FL457291
EST:     GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211364888|gb|FK992237.1|FK992237
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|28987432|gb|CB351631.1|CB351631
EST:     GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|67016374|gb|CO445123.1|CO445123
EST:     GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211362236|gb|FK992224.1|FK992224
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211174474|gb|FL037930.1|FL037930
EST:     GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: GTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
EST: gi|211362241|gb|FK992229.1|FK992229
EST:     AAGCACAGGCAAGCTGGGTTGTGCTAGACAA                         GGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT
genomic: AAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatggtcaa ... tgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG
                  gcttaat  putative branch site (score: 4)
      attgttatttttgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC