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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcag

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgc--aagcacacaagtttacttta---------gtaaccactaccggcacagtatataccaactttttttttgactttctgcag
|||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||||||||   ||||     |||   ||||         || |    |   | ||| ||||  | | |       |   || ||  ||||
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatg-atccatacaaaatgcaacatttggcag

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 21
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagcacac-aagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcag
||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||  |||| |||||||||||| ||||||||||| ||      || |||  || | |  |      ||  |   || |  |||  |  ||  |   |   |||| |   
TGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttttaaccaagggtattgtgttg-----tattgattcattgaatataactttactagctttgtttcag---

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 22
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgta----tgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttt-tttttgactttctgcag------------------
|||||||||||||| ||||||||||| || ||||| || || ||||| || ||||| || || |||||||| ||| |||| |||||     |   |   ||   |||||  ||  |    | | |        | |||   || | || ||||| |   | |  ||                  
TGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgttgctttatcatgtcatttgtttatattcctttgaagttctcttttcctttattttaaatattatttttaatactttttagaattcatatgagccattt

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcag
|||||||| || || ||||| ||||| || ||||||||||| || || ||||||||  |||| |||||||||||| ||||||||||| ||   |    || || |   || |      ||  |   || |  ||   |  ||  |   |   |||| |   
TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagc---cttttaacttaagggtattgttttgtattgattcattggatgtaactttactagctttgtttcag---

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 5'ss of exon 22
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcag---------------------
||||||||||| || |||||||| || || |||||||||||  |||||||||| ||||| || || || || ||| |||||||||||||     | ||  ||| |    ||    || |||| |   | || |   |   ||| ||| ||| | |||   |                     
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAGgtatgttgctagac--gttaagaacagctctca-tacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtag

upper sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 23
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaacttt-ttttttgactttctgcag
|||||||| || || ||||||||||| ||||| ||||||||||| || |||||||| || || |||||| ||||| | ||||| ||  ||   || | || | |  ||   ||   | |    ||    | | | |   || | || ||||  |      ||
TGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAAgtgagctt-catataactctttttgtttatatattgtttgcttcctctctgcttgctatattctttgtttggtcttag

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|58029637|gb|CX725064.1|CX725064
EST:     TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|32920203|gb|CF025015.1|CF025015
EST:     GTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: GTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|32934898|gb|CF039710.1|CF039710
EST:     TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|32920665|gb|CF025477.1|CF025477
EST:     TAAAATAGCACCCAGTGTTATATTTATTGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcag

- - - - - - - - - - - - - - - - - - - - - - AGCAAG