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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgctcttacgcgtgccattgatagaaaaaccctctgcatggttttcaccggcttcgttgctctcag

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 25
AATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgctc-ttacgcgtgccattgatagaa----------aaaccctctgcatggttttcaccggcttcgttgc--tctcag
 ||||| |||||||| |||||||| |||||| |||   | | | |||||||||| || ||||||| |||||| ||||| ||||||||||| |||||||||||| | ||| |  | | |||   |    |||  |           ||     ||||   ||||||| | |||  |||   || |||
GATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTTGCCACTATGACCGATGGATATTCAGGAAGTGACCTGAAGgtatgcttgataatgatgcgcttcccaaataacacaagtgattggaaatggttgcacaattttcactgacttgcttgtgttcccag

upper sequence: GRMZM2G126453_T01 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 21
AATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgt-acgtttg-------ctcttacgcgtgccattgata---gaaaaaccctctgcatggttttcaccggct--tcgttgctctcag-------
|||| | | ||| ||||| |||||||||||  ||| | ||||||||||| | ||  |  | || |||||||||||||| ||||||||||| ||||| |||||    |||        || ||||        |||||    |   ||            |  |||  | ||  | |||    |  |       
AATTGTCAGAGTTATTTTAGCAAAAGAAGATTTGGCACCTGATGTTGATTTTGAAGCAATAGCAAATATGACTGATGGATATTCAGGAAGTGACCTAAAGgttgtatttctatatatcttttacttcaattcttgatcactggggaagatgacatgaaatactcattgactcattgttatcttttgactgcag
















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|211384433|gb|FL031621.1|FL031621
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAG
EST: gi|32921157|gb|CF025969.1|CF025969
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
EST: gi|32920203|gb|CF025015.1|CF025015
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
EST: gi|211048841|gb|FL187601.1|FL187601
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
EST: gi|211048838|gb|FL187598.1|FL187598
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAA
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAA-TCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAA
EST: gi|32921345|gb|CF026157.1|CF026157
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
EST: gi|211048837|gb|FL187597.1|FL187597
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
EST: gi|32920665|gb|CF025477.1|CF025477
EST:     TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAG                         AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG
genomic: TGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgc ... ttgctctcagAATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTTGCCAATATGACTGATGGTTATTCAGGAAGCGACCTGAAGgtacgtttgctcttacgcgtgccattgatagaaaaaccctctgcatggttttcaccggcttcgttgctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG