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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctaatattctttcttcaatttagcctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG

Basic information

species Zea mays
transcript GRMZM5G833389_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g60190.2 (Oryza sativa), 3'ss of exon 3
----------gtttgctaatattctttcttcaatttagcctg--gttcagttactgcca---caagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG
           | || | |    |    |  | |  |   ||  ||| | |||||| ||       | ||  | |  | | |||    || | | ||| | ||||||||||||| ||||||||| || || |||| ||| ||||| ||||| |||||||||||||| |||||||||||||| |||||| ||||||| |
gtttgttaagctctgatgaatggcgccttatattgcaatgtgttgtttatttactgtcaatttttaaattggtgtgttctgtttcactctat-ttcagCTGCTTCTGAAAGGTGCCAGTGAGAGGGGAGCAAAAAGAATTCGTGTTCACATTCTTACTGATGGACGCGATGTTTTGGATGGCAGCAGTGTTGGTTTTG

upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
------gtttgctaa--tattctttcttcaatttag--cctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG
       |||| ||   | ||| || ||   || |    |||||| | |   ||    | ||||   || || || ||   |  | |   |||||  |  | |||||      |||  | || || || | |||| | || || || ||||||||||| |||||||||||||||||    ||| |||| || |
gttttgatttgatatgttcttcattattttgttcaaattctggtttaatgtttgttg-atgattcctta-aacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG

upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
--gtttgctaatattctttcttcaatttagcctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG
    ||  |  |  ||| |     ||||    ||   | |||   |       |||| || ||||||  ||  |  |   | ||||| || || || ||| |    ||  | || || || | |||||| || || || ||||||||||| |||||||||||||||||    ||| | || || |
gtacttaattctcatctgttacacatttcttttgaaac-gttggcgtttgttaattttctttaatttggttctg-tttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG

upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 3
---------gtttgctaatattctttcttca--atttagcctggttcagttactgccacaagatttactataatttttttggggctctatcc-----agTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG
         |||    |||  | || | |    |||     | |||  ||   | |||   ||   |  || ||  | || ||  | |   |     |||||||| | ||||| |  |||||||  || || |||| ||||||||| || |||||||||||||| |||||||||||||||||   |||| |||| || |
gtatgttttgttgttgaattctattaccttgtgattggatatagttttgtatttcccaggggag--atcatgatcctctttggctttttctcttggcagTTACTTTTAAAAGGAGCTAGTGAGAATGGTGCAAAAAGAATCCGTGTCCATATCCTTACTGATGGGCGTGATGTTTTGGATGGTTCCAGTGTTGGGTTTG

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|71330938|gb|DR802276.1|DR802276
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC
EST: gi|33102738|gb|CF062698.1|CF062698
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCNNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC
EST: gi|32838945|gb|CD978626.1|CD978626
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC
EST: gi|33102662|gb|CF062622.1|CF062622
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC
EST: gi|33101245|gb|CF061205.1|CF061205
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC
EST: gi|6526987|gb|AW216215.1|AW216215
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC
EST: gi|33102595|gb|CF062555.1|CF062555
EST:     TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAG                         TTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCNNNNNNNNTCCGTGTGCAC
genomic: TTGGGTTGTTGAGTGATGGTGGTGTCCACTCCCGTCTTGATCAACTGCAGgtttgctaat ... ctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG
                                             ctctatcc  CT-rich tract
                  acaagatttactataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctaatattctttcttcaatttagcctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG