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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcactgtgacctgcgggccgactccccccacctccagcccgagttcttgcattatgctgaaaatgttcagatgtatgtaaatagttctgctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATTGGCTGACTTCGGAATGGCAAAGCAT

Basic information

species Zea mays
transcript GRMZM2G156800_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156800_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g55560.2 (Oryza sativa), 3'ss of exon 5
tggcactgtgacctgcgggccgactccccccacctccagcccgagttct----tgcattatgctgaaaatgttcagatgtatgt-aaatagttctgctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATTGGCTGACTTCGGAATGGCAAAGCAT
        |    |     |    |||       |  ||   ||  | |    ||||| |||||||||  || || |||||  | ||||  || | ||||||||| ||||||||||| ||||||||| | |||||| | || |||||||| |||||||||||||| |||||||| ||||||
-----aaatatttttttctcaagttcctttgttatttagtttgaactttggactgcatgatgctgaaagagtacacatgtaaatgaaatcattatactcttgcagAGATATCAAAGGAGCAAATTTGCTTGTTGATGTGAATGGTGTAGTCAAATTGGCTGACTTTGGAATGGCTAAGCAT
















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|87156020|gb|DY400809.1|DY400809
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|26559130|gb|CA831365.1|CA831365
EST:     CATATTCTCAAGGGGCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGAGAAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|22542085|gb|BU092523.1|BU092523
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|60345120|gb|DN212093.1|DN212093
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|22473422|gb|BU037902.1|BU037902
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|50338068|gb|CO533194.1|CO533194
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|87157200|gb|DY401989.1|DY401989
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|26558715|gb|CA830950.1|CA830950
EST:     CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
EST: gi|6031429|gb|AW076331.1|AW076331
EST:     CATAGGGTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAG                         GGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT
genomic: CATATTCTCAAGGGTCTTGCTTTTTTACATAGCCAAAAGATTATGCATAGgtaattattt ... gctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgcattatgctgaaaatgttcagatgtatgtaaatagttctgctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATTGGCTGACTTCGGAATGGCAAAGCAT
                                         ttctgctctt  CT-rich tract
                              tatgtaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcactgtgacctgcgggccgactccccccacctccagcccgagttcttgcattatgctgaaaatgttcagatgtatgtaaatagttctgctcttgcagGGATATCAAAGGGGCAAATTTGTTAGTTGATATTAACGGTGTAGTGAAATTGGCTGACTTCGGAATGGCAAAGCAT

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