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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatcattattacttaattttatttatttattgcggttcttttttatgcaatttatcttctgtcattctaacaaatgtgtacctttttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTTGGGGAAATGTTCCGTGAGAGGCAATTGGCTCATTGGCTGAAAGCTGAGA

Basic information

species Zea mays
transcript GRMZM2G452529_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G452529_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 11
gtgaggatcat-tattacttaattttatttatttattgcggttcttttttatgcaatttatcttctgtcattctaacaaatgtgtacctttttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTTGGGGAAATGTTCCGTGAGAGGCAATTGGCTCATTGGCTGAAAGCTGAGA-
|| |||| |||   | | || |   | |||| | ||||        | || ||  |||   ||| ||   |||  |          | ||| |||| |||||| ||||||| ||||||| ||||||||| ||||   ||||| | || ||||||||||| | |||||| ||||||||    ||   ||||| | ||     
gtcaggaccatgcttcatttgagcctgtttact-attg--------tcttgtgtgatt---cttatgcatttccgat---------cttttgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTTGGGGAAATCTACCGTGAAAGGCAATTAATGCAG-AGCTGAGAACTAGTTT
















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|5871566|gb|AW018037.1|AW018037
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|60348342|gb|DN215315.1|DN215315
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|88753935|gb|DY538076.1|DY538076
EST:     AATCATTCATTGCACCTCAGAACTTTTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|211372465|gb|FL432864.1|FL432864
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|7145231|gb|AW506712.1|AW506712
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|6031444|gb|AW076346.1|AW076346
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|78021196|gb|DV489583.1|DV489583
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|5915325|gb|AW052966.1|AW052966
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGANCAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
EST: gi|78023335|gb|DV491722.1|DV491722
EST:     AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT
genomic: AATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatca ... tttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatgcaatttatcttctgtcattctaacaaatgtgtacctttttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTTGGGGAAATGTTCCGTGAGAGGCAATTGGCTCATTGGCTGAAAGCTGAGA
                         ttctaac  putative branch site (score: 1)
                                       tacctttttcattc  putative PPT
         aatttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggatcattattacttaattttatttatttattgcggttcttttttatgcaatttatcttctgtcattctaacaaatgtgtacctttttcattcagATTATAAGAAACCTAACCTATGAGGAGCAAAAATATGTATATGAACAACTTGGGGAAATGTTCCGTGAGAGGCAATTGGCTCATTGGCTGAAAGCTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA