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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcgtgcttatatatgggagggctagcgcgtaatgccgacttttttcctcaagcaaaatgtggtttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCA

Basic information

species Zea mays
transcript GRMZM2G003565_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003565_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g35570.3 (Oryza sativa), 3'ss of exon 7
---------------gtatggcgtgcttatatatgggagggc-tagcgcgtaatgccgacttttttcctcaagcaaaa------------------tgtggt-ttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCA----
               | | |      | |  ||| | ||     |   | ||||  | |  ||| | ||||| ||| |                  |||| | |||| ||||||| |  |||| ||||| ||||| |||||||||||||| ||  |  | || ||||||||||| ||||| ||||||||||| ||||||||||| || ||      
gtatggcatatatctggaggaataaatgaactattgaagcatacaagtcataatcacaatatttatgctcaatcaagaacttgatgttccatttcttgtgttgttgctgcagaaagTTGCCCAAGTTGCTTGCGGGTGGAGGCATACTCTTGCATTTACAGAAAAGAAAAATGTTTTCTCATGGGGGAGGGGTACTAGCGGACAACTTGGTCATGG

upper sequence: GRMZM2G003565_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g35570.2 (Oryza sativa), 3'ss of exon 7
---------------gtatggcgtgcttatatatgggagggc-tagcgcgtaatgccgacttttttcctcaagcaaaa------------------tgtggt-ttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCA
               | | |      | |  ||| | ||     |   | ||||  | |  ||| | ||||| ||| |                  |||| | |||| ||||||| |  |||| ||||| ||||| |||||||||||||| ||  |  | || ||||||||||| ||||| ||||||||||| ||||||||||| || ||  
gtatggcatatatctggaggaataaatgaactattgaagcatacaagtcataatcacaatatttatgctcaatcaagaacttgatgttccatttcttgtgttgttgctgcagAAAGTTGCCCAAGTTGCTTGCGGGTGGAGGCATACTCTTGCATTTACAGAAAAGAAAAATGTTTTCTCATGGGGGAGGGGTACTAGCGGACAACTTGGTC
















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|29130842|gb|CB381546.1|CB381546
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
EST: gi|211087172|gb|FL255715.1|FL255715
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
EST: gi|194716840|gb|FK933999.1|FK933999
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCACAGGTTGCATGCGGATGGAGGCACACTCRGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
EST: gi|60342864|gb|DN209837.1|DN209837
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
EST: gi|211471127|gb|FL255671.1|FL255671
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
EST: gi|211476174|gb|FL255694.1|FL255694
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCCCAGGTTGCATGCGGATGGAGGCACACTCTGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
EST: gi|60339276|gb|DN206249.1|DN206249
EST:     ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAG                         AAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG
genomic: ACAACGACGACCACAGCTCCCCCGGACAAGTCAGTTTTCCAGAGGATCAGgtatggcgtg ... tttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggctagcgcgtaatgccgacttttttcctcaagcaaaatgtggtttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCA
                    actttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcgtgcttatatatgggagggctagcgcgtaatgccgacttttttcctcaagcaaaatgtggtttgccgcagAAAATCTCCCAGGTTGCATGCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC