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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcag

Basic information

species Zea mays
transcript GRMZM2G127050_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127050_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 5'ss of exon 7
TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcag
||| || |||||||| || |||||||| ||||||||  |||| || |||||||||||||||||   ||| |||||||| |||||||||||||  || ||||||||  |   ||||| ||   || |||     ||   | |  |   |   | | | | |      | |  |  | || | ||||
TCTATCCCCCATGGGTGAAGCCTGTTCTAGGATGGACATGACAGCAATCCATCAGATTCTAGTTGCCACACATTACAGAGATGATGAAGGGACTAATGAGgtaaat-attggagcactttgatttctgtcatatggcagatcgttgtctaagaaatctatctcttcatcaatctccctgttgcag
















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|76013660|gb|DT940830.1|DT940830
EST:     ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|71310550|gb|DR791570.1|DR791570
EST:     ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGCAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|32919403|gb|CF024215.1|CF024215
EST:     ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGGACGCAGCAGATGAGGGACATGCTGGAAGCTAG
genomic: ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGG-ACGCAGCAGATGAGGGACATGCTGGAAGCTAG
EST: gi|149059663|gb|EE157007.2|EE157007
EST:     ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|32919355|gb|CF024167.1|CF024167
EST:     ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|76015318|gb|DT942488.1|DT942488
EST:     GGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGTTAGG
genomic: GGGAGCAACGAGgtaaaagacc ... tctatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTCTCCCATGGGCGAGGCCTGTTCCAGGATGGATCTGACTGCCATCCATCAGATTCTAGTGAACACGCATTACAGGGATGATGAAGGGAGCAACGAGgtaaaagaccagagcatttctgttgctgctgcctgctggcttctccacagggtactatctaagaaaaacggtgcctctatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA