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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaattttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgcttgctgctaggtcttagagagctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccag

Basic information

species Zea mays
transcript GRMZM2G108457_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108457_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 12
GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaattttactgtgtctgtcactgaacagggat--agcttaatgtttcagcaagatagaattagtcacgtgctt-gctgctaggtcttagagag-ctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccag
||| | ||||||||||| |||||||||||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||| ||||| || || |||||||||||||| |  || |  |  |   | |  || | | |   || || | |  |  | |   |    |  || | |  ||| |   ||| |   |||||||  |   ||   || ||||||   || |   ||  |    ||   |  |  | | ||| |||||||   | |  |||||
GGCTTGTACTGTGTTGGCGACAGCTGTTTTCCTGGGCAAGGTGTAATTGCTGTGGCATTTTCAGGGATCATGTGTGCTCATCGAGTTGCAGCTGATATTGgtaagttcagattccactaacatccccctaaaatgaactgagtttgaaggattgggagctttatttatgttagggtcttagggactaagaagtagagagatttgtctgctgatgaacaaca-taagctgatattggcagaaaaatgacgtttgtttgctgctttgatcctcatccag

upper sequence: GRMZM2G108457_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA10G10990.1 (Glycine max), 5'ss of exon 12
GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaa--ttttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgcttgctgctaggtct-tagagagctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccag
|| ||||||||||||||||| ||||| || || ||||||||||| || |||||||| ||||||||  | ||||| ||||| ||||| ||||| |||||||||||| ||     || ||     |||  |   |||   |||||  ||  ||||    | ||      |  | | | |||  ||||     |  | | || |                                                                           
GGTCTTTACTGTGTTGGTGATAGCTGCTTCCCTGGACAAGGTGTTATTGCTGTAGCTTTCTCAGGAGTTATGTGTGCTCATCGAGTAGCTGCTGATATTGgtaagatagagcattccttcaaatgt-gcaacacattaatagc--aagctttccttcaaattctggcaaacccttacttaatgcttcaaatgcacaaagttat-------------------------------------------------------------------------

upper sequence: GRMZM2G108457_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G34060.1 (Glycine max), 5'ss of exon 12
GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaattttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgcttgctgctaggtct-tagagagctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccag
|| |||||||||||||| || ||||| || || ||||||||||| || |||||||| ||||||||  | ||||| ||||| ||||| |||||||||||||||||| ||     | |   ||     |  ||||     |    ||  ||||    | ||      |  | | | |||  ||||     |  | | || ||                                                                          
GGTCTTTACTGTGTTGGCGATAGCTGCTTCCCTGGACAAGGTGTTATTGCTGTAGCTTTCTCAGGAGTTATGTGTGCTCATCGAGTAGCTGCAGATATTGgtaagatagacc-attccttcaaatgcaaaacacattaatagcaagctttccttcaaattctggaaaacccttacttaatgcttcaaatgcacaaagttgt-------------------------------------------------------------------------

upper sequence: GRMZM2G108457_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0032g00800.t01 (Vitis vinifera), 5'ss of exon 12
GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaattttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgcttgctgctaggtcttagagagctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccag
|| || ||||||||||| || ||||| ||||| ||||||||||| ||||||||||| || |||||  | ||||| || |||||||| |||||||||||||||||| |   |||   | | |||         |   || ||||       ||   |  |  |||   ||   || || ||  |    |||      ||||||| |                                                                    
GGTCTCTACTGTGTTGGGGATAGCTGCTTTCCAGGACAAGGTGTTATAGCTGTAGCCTTTTCAGGTGTAATGTGTGCACACCGAGTGGCTGCAGATATTGgtaagctgggttt-tagagactgctttattgtaaaaattgcttggc----cattgacttgaaatatatccattgatttcttgtgaaacttg----cctgaactatttta----------------------------------------------------------------

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|149086468|gb|EE176013.2|EE176013
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|71431774|gb|DR812824.1|DR812824
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|211081518|gb|FL472798.1|FL472798
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|60336973|gb|DN203946.1|DN203946
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|86471657|gb|DY238027.1|DY238027
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|166615281|gb|EG315468.1|EG315468
EST:     GGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGTTGGTCTTCTTGGGCTACTCA
genomic: GGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaattttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgcttgctgctaggtcttagagagctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT