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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtcatgcatatgatggcaaagttagatagttggattgggattgcacttatatttgcctaatttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTGAAGAAGGGTGTTCTTCCTTGGCACATACTCTTTGGGCTCTTTGTCTACA

Basic information

species Zea mays
transcript GRMZM2G066885_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066885_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g42890.1 (Oryza sativa), 3'ss of exon 3
---------------------------gtaaggtcatgcatatgatggcaaagttagatagttggattgggattgcacttatatttgcctaatttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTGAAGAAGGGTGTTCTTCCTTGGCACATACTCTTTGGGCTCTTTGTCTACA
                           || ||    |   | | ||    || ||   | | | | |    | | |   || | |   |   | |||  ||||||||| | || || ||| | |||||||||||  ||||| |||||| ||||| ||||||||||||||||||||| ||||| ||||||||||| |||||||
tttattgtagtagttgatatctgcccggtgaga--gttttttttatatataactttacttgattgttgacaacttcttgtaaaatgcgcctgtctattgcagTGGATATTCGGGTTTGTTGCTTTCTTCTTCCCCCGTGCTTCGCCAAGCGTGAGGAAGGGTGTTCTTCCTTGGCATATACTGTTTGGGCTCTTCGTCTACA
















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|211096758|gb|FL470670.1|FL470670
EST:     GTCTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
EST: gi|211055163|gb|FK977534.1|FK977534
EST:     GTCTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
EST: gi|148965066|gb|EC906072.2|EC906072
EST:     GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
EST: gi|50323144|gb|CO518270.1|CO518270
EST:     GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
EST: gi|211055161|gb|FK977532.1|FK977532
EST:     GTCTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
EST: gi|148946110|gb|EC891404.2|EC891404
EST:     GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
EST: gi|76287729|gb|DV027297.1|DV027297
EST:     GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAG                         TGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG
genomic: GTTTGCACTCTTGGATTGGGATAGGGACGATTACTTTGTATGGTATTCAGgtaaggtcat ... tttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaagttagatagttggattgggattgcacttatatttgcctaatttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTGAAGAAGGGTGTTCTTCCTTGGCACATACTCTTTGGGCTCTTTGTCTACA
                                       gcctaat  putative branch site (score: 3)
                             acttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtcatgcatatgatggcaaagttagatagttggattgggattgcacttatatttgcctaatttatcacagTGGATAGTTGGATTCGTTACATTCTTCTTCCCTGGTGCTGCGCCAAACGTGAAGAAGGGTGTTCTTCCTTGGCACATACTCTTTGGGCTCTTTGTCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG