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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcacaaaatgtttacttgtttctgcagctatcttttaaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg...

Basic information

species Zea mays
transcript GRMZM2G056975_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 6
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcacaaaatgtttacttgtttctgcagctatcttttaaattttttattgttatgcatatttggtgtaaagttgggaaa-----gtacatgct-ggctttgg-
||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| |||||||||||||||||||| |||||||||||| | || |||||   |     |  ||| | |||  |||  | ||  ||  | | ||  |  |||||||||| |||| || |     |||| | ||   | |||  
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGCACAAAGTGAAAATACTTCCTGCTGATTCTGAGCACTCTGCTATATTTCAGgtaccacagaaaataaat-----tacctgtaactaatttt--acttggttcatctgatataagtttggtgtaaggttgtgatagtctggtacgtactcaacgttgcc

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 6
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcacaaaatgtttacttg-------tttctgcagctatcttt-taaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg------------------------------------------------------------------------
||||||| | ||||| || ||||||||||| ||||| ||||| || || || || || ||||| |||||||||||||| || || ||||| || ||||||||||      | ||  | | ||        | | |||| | |  |   || |  |  |  ||||||  ||  |   | ||   |  ||     ||||      | | |                                                                        
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatggatataatcaattaaaaaatttgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctccacatctctcttattgcgtgcaagcaattattttatcatctgctccacttggtactgcaaaagcttaaaggattcttgttggcttcag

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 6
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaa---ctcacaaaatgtttacttgtttctgcagctatcttt-taaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg------------------------------------------------------------------------
||||||| | ||||| || ||||||||||| ||||| ||||| || || || || || ||||| |||||||||||||| || || ||||| || ||||||||||     ||||||  ||  |    | | |||| | |  |   || |  |  |  ||||||  ||  |   | ||   |  ||    | |||  |   | | |                                                                        
AGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGCATAATGTAAAAATACTTCCAGCTGATTCAGAACATTCTGCCATCTTTCAGgtaagaatgcacaaatagtaaaaaattgtgtgcaacaagatgaatagacatgctcatgttatttattatctatatattctctggcctctgcatctttcttattgcatgcaagcaattattttatcatccgctccacttggtaatggaaaagcttaaaggattcttgttggcttcag

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 6
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcacaaaatgtttacttgttt-ctgcagctatctt-ttaaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg---------------
||||||| | || |||||||||||||| |||||||| |||||  ||||||| || || || |||||||| || ||||| || || ||||| |||||||||||| | || |  |  |  | ||   | |  || || || | || | ||     ||| | |  ||    | |  |    ||| ||  |   ||     | |                 
AGAGACATTAATCGCAGGTGGTCCTTTCGTGCTTCCGCTTGCCAACAAACATAATGTAAAGATTCTTCCGGCAGATTCAGAACATTCTGCCATATTTCAGgtatcacaaatcacatagaattaagtacctcaactttcatattgagttcagcgttggtcttaatgcaagttcaacctctggcaatttgagtgaaaaatcttcttttatgttctctag

upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 6
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcacaaaatgtttacttgtttctgcagctatcttttaaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg
|||||| || ||||| || ||||||||||| ||||| ||||||||||| ||||| || || || ||||| ||||| || || |||||||||||||||||||||    |  | || |  |||  |  ||     || ||||| ||||  |   | || || | | |   | ||   |    | | | |  | |    || |
AGAGACCCTAATTGCTGGGGGTCCTTTTGTCCTTCCTCTTGCACACAAGCACAATGTAAAGATCCTTCCTGCTGACTCAGAACACTCTGCAATATTTCAGgtagggaagcatatctacactgatagctaattttagcttttcaattcatgtgtattgtgtacaatgcatatatgttaattataatgctggattatctttg

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|71445035|gb|DR826085.1|DR826085
EST:     ACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAG                         TGTATACAAGGCTTTGTC-GAAAGTGCACTTCGTCGCATTATTCTAACTGC
genomic: ACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcaca ... cttgtaccagTGTATACAAGGCTT-GTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGC
EST: gi|14206809|gb|BG840487.1|BG840487
EST:     ACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAG                         TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCA
genomic: ACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcaca ... cttgtaccagTGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCA
EST: gi|211496438|gb|FL049443.1|FL049443
EST:     ACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAG                         TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCA
genomic: ACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcaca ... cttgtaccagTGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAACACAAAGTGAAAATTCTTCCAGCTGATTCTGAGCACTCTGCAATATTTCAGgtaactcacaaaatgtttacttgtttctgcagctatcttttaaattttttattgttatgcatatttggtgtaaagttgggaaagtacatgctggctttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT