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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgcctttagtacttttgtgcatttccatgttatagacattttatgctgaatattatgcattaattttgttccag

Basic information

species Zea mays
transcript GRMZM2G080083_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080083_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 5'ss of exon 9
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgcctttagtacttttgtgcatttccat---gtta---------tagacattttatgctga-atattatgcattaattttgttccag
||| |||||||||||||||||||||||||| |||||||||||||||||||| || ||||| |||||||||||||| || |||||||||||||||||||||||  ||   |  | |||| || ||||| ||   ||||         ||| | ||||| ||||| ||||| |   ||  | ||||| |||
CTTTTTTGAGGAGCAACTTCATCGCATGGAATGCATGGCCCAGGAACCTGTACTGTTTGAAGACATCTTGTGTCAACTAATTGATATGATTGGACCTGAGgtaacca--aacatttttctgtatttctattctgttactaggttcttaggctttttaagctgatatatt-taatttgttcttgtttcag

upper sequence: GRMZM2G080083_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgccttt--agtacttttgtgcatttccatgttatagacattttatgctgaatattatgcattaattttgtt-ccag----------------------------------------------
 || |  ||||||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||| | |||||  | |  |||||||| |||||||  ||   | ||  |||| | |  |  |  |   |    |    |||  |         |   ||||| ||||   | | ||                                              
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag

upper sequence: GRMZM2G080083_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgt------tgcctttagtacttttgtgcatttccatgttatagacattttatgctgaatatt--atgcattaattttgttccag------------------------------------
 || |  ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||| ||  |  | |||||  |   ||| ||||| || || | |||      |  |||| | |  ||||| ||  | |||  | |        |    | | | ||  ||| |||  |        ||                                    
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGTATGGCTCAGGAGCCTGTTCTTTTTGAAGATGTTGTTTGTCAAATGGCTGACATGATAGGGCCAGCGgtaagcatttgcttttgaagatttgtacaagttcattctcttccttgagttgctttagtgttcaatgaattggtcggtacttagcatgggtgtattgttgacatctacccttcactgcag

upper sequence: GRMZM2G080083_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgcctttagtact-----tttgtgc-atttccatgttatagaca-----ttttatg------ctgaata--ttatgcattaattttgttccag--------------------------------------------
 || | |||||||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||| | |||||  |    || ||||| ||||||| |||   |||| |   |     |||||   | | | || || |  |||     | | | |      ||||| |  |  ||| | || ||  |  | |                                            
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag

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|6020789|gb|AW065717.1|AW065717
EST:     TTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAG                         AATGATAGCTATTTGACATTGAAAGACTTCCGAAGGTGCAAACTGTCTGGA
genomic: TTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgccttta ... tttgttccagAATGATAGCTATTTGACATTGAAAGACTTCCGAAGGTGCAAACTGTCTGGA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgcctttagtacttttgtgcatttccatgttatagacattttatgctgaatattatgcattaattttgttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA