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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGCTTTGCATGGGTTCTTCGATATTCTTTTGCTCTCTTAGGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatatttttctcgtctttgtagttgcaaatcaaagtagtttctgacatatggttgcactgcaattgcatatgtggggatggtgtgtggattctgc...

Basic information

species Zea mays
transcript GRMZM2G116282_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116282_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g52390.1 (Oryza sativa), 5'ss of exon 5
CTGAGCTTTGCATGGGTTCTTCGATATTCTTTTGCTCTCTTAGGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatatttttct-cgtctttgtagttgcaaatcaaagtagtttctg-acatatggttgcactgcaa----ttgcatatgtggggatggtgtgtggattctgc
                                           |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||    | ||   | |||  |  | |    |  |  |   | | |  | |  |  |  || |   |||    ||| | || || || |  |||    |      
-------------------------------------------GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaacttacatacgtagtaattggcagacctttacacattcttcgtaggtcagtctggatgccaaaatcttgtaaatttgaggttcttgtacaca------
















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|211148667|gb|FL386510.1|FL386510
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|87157115|gb|DY401904.1|DY401904
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|60344109|gb|DN211082.1|DN211082
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|24766808|gb|CA401955.1|CA401955
EST:     ACAAGGATAAGAAGAAGGAAAATCCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|24767436|gb|CA402578.1|CA402578
EST:     NCAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|32939360|gb|CF044179.1|CF044179
EST:     AAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: AAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|113574804|gb|DW747819.1|DW747819
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTTAAGG
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGG
EST: gi|15177350|gb|BI398289.1|BI398289
EST:     GAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: GAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|22472972|gb|BU037452.1|BU037452
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|78074541|gb|DV502975.1|DV502975
EST:     AAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: AAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|22472627|gb|BU037107.1|BU037107
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|37391508|gb|CF632997.1|CF632997
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|86467836|gb|DY234206.1|DY234206
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|24764617|gb|CA399781.1|CA399781
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
EST: gi|62525866|gb|DN828514.1|DN828514
EST:     GGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG                         TCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC
genomic: GGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatat ... tggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGCTTTGCATGGGTTCTTCGATATTCTTTTGCTCTCTTAGGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAGgtatgcatatttttctcgtctttgtagttgcaaatcaaagtagtttctgacatatggttgcactgcaattgcatatgtggggatggtgtgtggattctgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG