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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggctctcctttttttttttctctttgccgcaagcgctatgggatctgcgaatggtggtggcctcggtttgttaaagggtcgagcgtttgtttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAGCGCGTCGCCGTGAAGTACTACAGCGATGGCTGGCCTACTCTCTCCGCGA

Basic information

species Zea mays
transcript GRMZM5G883149_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G883149_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 1
---cggctctcctttttttttttctctttgccgcaagcgcta--tgggatctgcgaatggtggtggcctcggtttgttaaagggtcgagcgtttgtttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAGCGCGTCGCCGTGAAGTACTACAGCGATGGCTGGCCTACTCTCTCCGCGA
    ||||| || ||| ||  || ||    | ||| | || |   ||||||| ||  || || | |        ||     |  | ||  ||||| | | | |||||  ||| ||| ||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||||  ||||  |||||||||||||| ||||
gctgggctccccgtttcttggttttc---acggcaggtgcaaatcgggatct-cgtttgttgttagttagttgatggcgttgctttgatggtttgctcg-tacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA
















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|211025061|gb|FL063409.1|FL063409
EST:     CTCCGCTCCCCGCCGTGAATCCTTCCTCCTCCCGCGATG                         GAGACCTTCCCGTTGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
genomic: CTCCGCTCCCGGACGTGAATCCTTCCTCCTACCGCGATGgtaggtggtc ... tttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
EST: gi|211025062|gb|FL063410.1|FL063410
EST:     CTCCGCTCCCCGCCGTGAATCCTTSCTCCTCCCGCGATG                         GAGACCTTCCCGTTGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
genomic: CTCCGCTCCCGGACGTGAATCCTTCCTCCTACCGCGATGgtaggtggtc ... tttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
EST: gi|211025063|gb|FL063411.1|FL063411
EST:     CTCCGCTCCCCGCCGTGAATCCTTCCTCCTCCCGCGATG                         GAGACCTTCCCGTTGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
genomic: CTCCGCTCCCGGACGTGAATCCTTCCTCCTACCGCGATGgtaggtggtc ... tttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
EST: gi|211477575|gb|FL100775.1|FL100775
EST:     CGACCACCGTCCTCCGCTCCCCGCCGTGAATCCTTCCTCCTCCCGCGATG                         GAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG
genomic: CGACCACCGTCCTCCGCTCCCGGACGTGAATCCTTCCTCCTACCGCGATGgtaggtggtc ... tttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcgaatggtggtggcctcggtttgttaaagggtcgagcgtttgtttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAGCGCGTCGCCGTGAAGTACTACAGCGATGGCTGGCCTACTCTCTCCGCGA
                                            gtttgat  putative branch site (score: 5)
                                         tttgttt  CT-rich tract
                      tttgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggctctcctttttttttttctctttgccgcaagcgctatgggatctgcgaatggtggtggcctcggtttgttaaagggtcgagcgtttgtttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAGCGCGTCGCCGTGAAGTACTACAGCGATGGCTGGCCTACTCTCTCCGCGA

- - - - - - - - - - - - -tgccgca
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg