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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcctttggtaatcctcctttttatcaaagatttcaagtctttgcttgatacatgtgagaatgaatatgcttttctttctggttgctggtatgactttttcccctttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG

Basic information

species Zea mays
transcript GRMZM2G130889_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
gtaattcctttggtaatcctcctttttatcaaagatttcaagtctttgcttgatacatgtgagaatgaatatgcttttctttctggttgctggtatgactttttcccctttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG
             | | | |   | |     |||  |   ||||    | | || ||  |  ||   | ||      |  || |  ||| || ||| | |||||   || |         || ||||||||| ||||||| ||||| ||||||||||| ||||| || ||||||||||| || ||||||||||||||||||||||||
-------------tgaactttaatgtgtatgaagtctcatagtcaactcat-atccaaatc-gatcaattacagacatggtttt--ttgttgatataattttttgttctct---------tcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
















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|67028781|gb|CO457530.1|CO457530
EST:     CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
EST: gi|211104642|gb|FL379460.1|FL379460
EST:     CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
EST: gi|13125955|gb|BG316630.1|BG316630
EST:     CTGG-TACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
EST: gi|32849483|gb|CD989164.1|CD989164
EST:     CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
EST: gi|60342116|gb|DN209089.1|DN209089
EST:     CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCA
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCA
EST: gi|32941898|gb|CF046717.1|CF046717
EST:     CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG                         CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT
genomic: CTGGTTACGGGCCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAGgtaattcctt ... catgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttctttctggttgctggtatgactttttcccctttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG
                           ctttttcccctttcca  CT-rich tract
                          acttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcctttggtaatcctcctttttatcaaagatttcaagtctttgcttgatacatgtgagaatgaatatgcttttctttctggttgctggtatgactttttcccctttccattcatgtcatagCTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA