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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttgtggaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcattttcag

Basic information

species Zea mays
transcript GRMZM5G868757_T07
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 4
TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgta-acctttgtggaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcattttcag--------------------
| |||||||||||||| | ||| || |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||||||||||||||||||||| | |||||     |  ||||||| ||||||| | | | ||||   |       ||  || | |  |    | |                    
TCCACAATGCTGCTCTCAGTGCTCAGCCAGCTTTGGTGCAGAATGAACGGAAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaactttgctacttgcttttcta-tgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtag

upper sequence: GRMZM5G868757_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 4
TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgta-acctttgtggaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcattttcag-------------------
| ||||| |||||||||| |||||| |||||||||||||||||||| || || ||||| ||||| ||||| ||||| |||||||||||||||||||||| |||   |||||     |  |||| ||   | |   | | |  | | |||   | | ||  ||    | |   |                      
TCCACAACGCTGCTCTTAGTGCACAGCCAGCTTTGGTGCAGAATGAACGAAAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgactttgctacttgcttttatatgacaagaacaaatgccctattccatcgttttctttcttctaaaccttgtgttctttttcatattgtag
















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|148948406|gb|EC893923.2|EC893923
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|6563772|gb|AW231304.1|AW231304
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         CCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|60395185|gb|DN228054.1|DN228054
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|194716906|gb|FK934065.1|FK934065
EST:     AAGCTGCTGGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|6020410|gb|AW065338.1|AW065338
EST:     AGCTGCTTGAGAAAATCAATATTCTTTGTCTGGA-GGAGATAATCTTTAG                         TCGGCCATCTGAAAATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AGCTGCTTGAGAAAATCAATATTCTTTGTCTG-ATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|148928048|gb|EC872430.2|EC872430
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|6020572|gb|AW065605.1|AW065605
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAAATAGAACTATTCCATTAA
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAA
EST: gi|32862654|gb|CF002336.1|CF002336
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAAATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|24765659|gb|CA400818.1|CA400818
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|149081819|gb|EE170978.2|EE170978
EST:     AAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|211013700|gb|FL252294.1|FL252294
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|148982850|gb|EE028700.2|EE028700
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|211117255|gb|FL447738.1|FL447738
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttgtggaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT