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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagctggccagcaagtgtataattttttattaagtactcaaaataaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA

Basic information

species Zea mays
transcript GRMZM2G179696_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 3
gtgagagctggccagcaagtgtataattttttattaagtactcaaaat--aaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
|| ||| ||  ||| | |   | ||   | | ||||  |||  | |||  ||||||| ||    |||    ||||| |||||| ||| || |||||||||||||||||||||||| ||||||||  |||||||||||
gtaagatctcaccatcca---tctagcatatcattatatacaaacaattcaaaagatggttcatttagtcacttaccttggatactt-ccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA

upper sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 3
gtgagagctggccagcaagtgtataattttttattaagtactcaaaataaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
|| ||| ||  ||| | | | ||  || |  |  ||   |  |||   ||||||| ||    |||    ||||| |||||| ||| || |||||||||||||||||||||||| ||||||||  |||||||||||
gtaagatctcaccatcca-tctagcatatcatcatatacaaacaattcaaaagatggttcatttagtcacttaccttggatactt-ccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA
















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|26559817|gb|CA832052.1|CA832052
EST:     AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACG                         TACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
genomic: AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACGgtgagagctg ... tttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
EST: gi|87157047|gb|DY401836.1|DY401836
EST:     AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACG                         TACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
genomic: AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACGgtgagagctg ... tttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
EST: gi|87156563|gb|DY401352.1|DY401352
EST:     AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACG                         TACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
genomic: AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACGgtgagagctg ... tttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
EST: gi|26560071|gb|CA832306.1|CA832306
EST:     AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACG                         TACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
genomic: AACAATGGTGGACCTACTCAGACACAGAAGACGAGGATGATGATGACACGgtgagagctg ... tttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcaaaataaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
                             tgcttac  putative branch site (score: 2)
                                          tgctttcct  putative PPT
     aaaataaaagatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagctggccagcaagtgtataattttttattaagtactcaaaataaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA